feat: mako module#12155
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matthdsm
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Jun 25, 2026
| tuple val(meta), path(bam) | ||
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| output: | ||
| tuple val(meta), path("${prefix}.bam"), emit: bam |
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Can we have maybe have this in one tuple?
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not sure about combining the BAM and BAI, because the .bai is optional: true but the .bam is always produced.
matthdsm
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Jun 25, 2026
| tuple val(meta), path("${prefix}.bam"), emit: bam | ||
| tuple val(meta), path("${prefix}.bam.bai"), emit: bai, optional: true | ||
| tuple val("${task.process}"), val('mako'), eval("mako --version | sed '1!d; s/^[^ ]* //; s/ .*//'"), topic: versions, emit: versions_mako | ||
| tuple val("${task.process}"), val('fgumi'), eval("mako --version | sed '2!d; s/.* //'"), topic: versions, emit: versions_fgumi |
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fgumi version is built into this command:
$ mako --version
mako 0.1.3 (rev unknown)
powered by fgumi 0.3.1
$ mako --version | sed '1!d; s/^[^ ]* //; s/ .*//'
0.1.3
$ mako --version | sed '2!d; s/.* //'
0.3.1
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PR checklist
Closes #12154.
This PR adds
makofrom Fulcrum Genomics, a faster replacements forsamtools sort.topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda