update gatk4,gatk4spark/applybqsr #1962
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| path fasta | ||
| path fai | ||
| path dict |
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:shake_fist: should have used the opportunity to update the meta here as well upstream
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I was half torn by that decision
| path "versions.yml" , emit: versions | ||
| tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true | ||
| tuple val(meta), path("${prefix}*bai"), emit: bai, optional: true | ||
| tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true |
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it;s annoying that no crai is created here. Is it one of the cases where they create the crai but call it bai?
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it's a possibility actually. I haven't checked that
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ok, so basically, if it's the case, then when a bai is created with a cram file we would just rename it to crai
That could be an opportunity to fix more inconsistencies for the index file naming
| } | ||
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| // Merge and index the recalibrated cram files | ||
| BAM_MERGE_INDEX_SAMTOOLS(bam_to_merge) |
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bam_to_merge doesn't seem to be set for the cram output
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ah seems to be a typo in the comment
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can all these bam operations not move into the if block? It should keep the terminal output cleaner
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Replaces #1911
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).