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Factor out preprocessing #1342
Factor out preprocessing #1342
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This PR is against the
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ch_name_replacements = ch_fastq | ||
.filter{ meta, reads -> | ||
reads.size() == 1 | ||
} | ||
.map{ meta, reads -> | ||
def name1 = file(reads[0]).simpleName + "\t" + meta.id + '_1' | ||
def name1 = file(reads[0][0]).simpleName + "\t" + meta.id + '_1' | ||
if (reads[1] ){ | ||
def name2 = file(reads[1]).simpleName + "\t" + meta.id + '_2' | ||
def name2 = file(reads[0][1]).simpleName + "\t" + meta.id + '_2' | ||
return [ name1, name2 ] |
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What's this whole change about?
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It's because I'm using ch_fastq directly (since the one with single
and multiple
branches is moved to the subworkflow). So these are now tuples output by groupTuple requiring the double index:
[[foo.fastq.gz,bar.fastq.gz]]
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I love this <3
Glad to hear- especially since you were skeptical about the subworkflow! |
Finally move preprocessing logic to the subworkflow, which I factored out of RNAseq to use in Riboseq.
I've had to update the subworkflow itself to incorporate some improvements related to strandedness, which we'd made in the meantime nf-core/modules#5982, so that will need merging first.
Edit: also nf-core/modules#5988
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).