Add WorkflowHub importer with per-tool workflow ID outputs

[paulzierep]

Add WorkflowHub importer with per-tool workflow ID outputs

Creates a new workflowhub-import/ importer that fetches all workflows from the WorkflowHub API and produces per-tool workflow ID files for the RSEc content repo.

What it does:

• Paginates through all workflows on WorkflowHub (~1500)
• Fetches detailed metadata for each workflow (title, creators, tags, EDAM annotations, license, DOI)
• Extracts tool names from two sources: curated bio.tools annotations and Galaxy internals.steps descriptions
• Maps tool names to data/{biotool_id}/ directories using galaxy_codex Suite ID → bio.tool ID mapping, falling back to raw tool name
• Writes data/{biotool_id}/{biotool_id}.workflowhub.json containing only a list of workflow IDs
• Saves full workflow entries to imports/workflowhub/{id}.workflowhub.json
• Supports --test [N] flag to limit workflows for testing
• Outputs stats: workflow count, tool distribution, and workflow engine breakdown (Galaxy vs Nextflow vs Snakemake etc.)

Usage:

# Full run (all workflows)
python3 workflowhub-import/workflowhub-import.py
python3 workflowhub-import/workflowhub-import.py --test 100   # Test with 100

# In the RSEc content repo
# The content repo has data/ with per-tool directories; the importer
# creates *.workflowhub.json files alongside existing *.biotools.json etc.

Format of per-tool files (e.g. data/fastp/fastp.workflowhub.json):

["1738", "1739", "1740", "1741"]

Instead of the workflow IDs we could also use links directly, it depends what is easier to add for the Atlas.
Unfortunatly most nextflow / snakemake workflows do not have tools available via workflowHUB api, I made some tests to get it via ro-crate or the associated github, but this is messy. I would opt to fix this rather on the workflow hub side.

[paulzierep]

linter fails due to other scripts alread merged !

[mihai-sysbio]

@rioualen @supernord just want to make sure you are aware of this, it would be great if you could consider reviewing