Support gzipped FASTA#162
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Co-authored-by: Copilot <copilot@github.com>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Co-authored-by: Copilot <copilot@github.com>
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Pull request overview
Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.
Comments suppressed due to low confidence (1)
workflows/variantcalling.nf:80
- The comment about adding a
.gzifor bgzip-ed genomes is now misleading in this workflow:ch_genome_uncompressedgunzips.gzreferences soSAMTOOLS_FAIDXwill never emit a.gzi(and thefa.name.endsWith('.gz')check will always be false). Update the comment (and/or the condition) to reflect the new uncompressed-reference behavior.
// generate fai that is used to determine the maximum length of chromosome
// also add the gzi if present as it is needed for bgzip-ed genomes
ch_genome_info = ch_genome_uncompressed
.join( SAMTOOLS_FAIDX.out.fai )
.join( SAMTOOLS_FAIDX.out.gzi, remainder: true )
.map { meta, fa, _no_fai, fai, gzi ->
def index_file = (fa.name.endsWith('.gz') && gzi) ? [fai, gzi] : fai
[meta + get_sequence_map(fai), fa, index_file]
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@copilot apply changes based on the comments in this thread |
Agent-Logs-Url: https://github.com/sanger-tol/variantcalling/sessions/62c07573-3dce-4a0f-a13d-51c39cd32a80 Co-authored-by: sainsachiko <134130358+sainsachiko@users.noreply.github.com>
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muffato
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May 28, 2026
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Check the latest gunzip module in nf-core. I think it extracts the name and extension the way you want to
muffato
approved these changes
May 28, 2026
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).