feat(modules): Convert preseq/lcextrap, qualimap/rnaseq, star/genomegenerate, subread/featurecounts, sylphtax/taxprof to topic versions #9826
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Convert the following modules from legacy versions.yml file emission to modern topic: versions channel emission: - preseq/lcextrap - qualimap/rnaseq - star/genomegenerate - subread/featurecounts - sylphtax/taxprof Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Use head -1 to get first line only, avoiding multi-line parsing issues. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove echo $(...) pattern which can cause issues. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Use tail -1 to get only the version, not the config warning. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Commands containing | and : need to be quoted in YAML. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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|
please split them up. it makes it easier to review if it is always the same version and version command |
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OK, fine, just let me get them passing here and I'll do it |
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Summary
Converts 5 modules from legacy
versions.ymlfile emission totopic: versionschannel emission (batch 2, following #9796).Modules converted:
preseq/lcextrapqualimap/rnaseqstar/genomegenerate(3 tools: star, samtools, gawk)subread/featurecountssylphtax/taxprofChanges
path "versions.yml", emit: versionswithtuple val("${task.process}"), val('toolname'), eval('...'), emit: versions_toolname, topic: versionscat <<-END_VERSIONSheredoc blocks from script and stub sectionsprocess.out.findAll { key, val -> key.startsWith('versions') }Test plan
nf-test test --profile docker🤖 Generated with Claude Code