Convert untar, pigz/compress, kallisto/index, samtools/index, bowtie2/build to topic versions #9796
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…/build to topic-based version emission
Converts these modules from versions.yml file emission to the modern
topic: versions channel emission pattern.
Changes per module:
- main.nf: Replace `path "versions.yml", emit: versions` with
`tuple val("${task.process}"), val('<tool>'), eval('<version_cmd>'),
emit: versions_<tool>, topic: versions`
- main.nf: Remove heredoc version blocks from script and stub sections
- meta.yml: Remove old versions output, add versions_<tool> output and
topics section
- tests: Update assertions to use findAll for versions outputs
- tests: Regenerate snapshots with structured version tuples
Updates 11 subworkflows to remove explicit version collection for
converted modules (versions now collected via topic channel):
- archive_extract
- bam_sort_stats_samtools
- bam_dedup_stats_samtools_umitools
- bam_markduplicates_picard
- bam_dedup_stats_samtools_umicollapse
- fastq_align_bwaaln
- bam_split_by_region
- fastq_remove_rrna
- fasta_index_dna
- fasta_index_bismark_bwameth
- fasta_index_methylseq
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Summary
Converts 5 modules from
versions.ymlfile-based version emission to the moderntopic: versionschannel emission pattern:Changes per module
path "versions.yml", emit: versionswith structured tuple output usingtopic: versionsscript:andstub:sectionsversions:output section, addversions_<tool>:output andtopics:sectionprocess.out.findAll { key, val -> key.startsWith('versions') }["PROCESS_NAME", "tool", "version"]Version output format
Before:
After:
Test plan
nf-core modules lint🤖 Generated with Claude Code