feat(modules): update all modules #1457
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SPPearce
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Apr 9, 2024
| BWAMEM1_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem | ||
| BWAMEM2_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem2 | ||
| DRAGMAP_ALIGN(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is dragmap | ||
| BWAMEM1_MEM(reads, index, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem |
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Why do these not want the fasta files?
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because we're not doing cram at that point yet
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Yes, but the fasta channel is already there, so why not just use it?
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useless if we don't create CRAM, and it would be a waste to store if not used
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But it'll only be passed as a symlink into the folder. Just don't see the reason to create a dummy variable for something that is already defined.
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I like the usage of [[id:'no_fasta'], []] as input here instead of the fasta, as it also makes it clear to me that BWAMEM1_MEM doesn't use the fasta.
Co-authored-by: Simon Pearce <[email protected]>
adamrtalbot
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Apr 9, 2024
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A lot of hidden diffs which I didn't check. Not sure what the changes are in the module configs?
SPPearce
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Apr 10, 2024
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Still not sure on the logic behind passing a dummy fasta rather than the actual fasta, but not going to get hung up about it.
adamrtalbot
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Apr 10, 2024
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PR checklist
nf-core lint).nextflow run . -profile 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).