Refactor - 3 #751
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Refactor - 3 #751
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Collaborator Author
| @nf-core-bot fix linting |
fellen31 reviewed Dec 3, 2025
Comment on lines +60 to +84
| .map { it -> | ||
| def meta = it[0] | ||
| def vcf = it[1] | ||
| def tbi = it[2] | ||
| | ||
| def hasRohCall = (it.size() == 6) | ||
| | ||
| if (hasRohCall) { | ||
| def rohcall = it[3] | ||
| def rohcallindex = it[4] | ||
| def interval = it[5] | ||
| return [ | ||
| meta + [prefix: meta.id + "_rhocall", scatterid: interval.baseName], | ||
| rohcall, | ||
| rohcallindex, | ||
| interval | ||
| ] | ||
| } else { | ||
| return [it[0] + [prefix: it[0].id + "_rhocall", scatterid:it[5].baseName], it[3], it[4], it[5]] | ||
| def interval = it[4] | ||
| return [ | ||
| meta + [prefix: meta.id, scatterid: interval.baseName], | ||
| vcf, | ||
| tbi, | ||
| interval | ||
| ] |
Contributor
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Is "it" really accepted here? Thought you would need .map { meta, vcf, tbi ...etc }. But difficult (impossible?) if there are variable number of elements. Is there any other way it could be written?
Collaborator Author
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Technically, parser seemed to accept "it". I expanded this block because it makes it clear what's happening here.
Nextflow doesn't support the spread operator for destructuring parameters in closures so it is not possible to expand the items when there are variable number of items. So something like {meta, vcf, tbi, *rest -> ....} doesn't work. Other solutions would probably add unnecessary logic which I don't want. 😅
Comment on lines 81 to 82
| .set { ch_for_mix } | ||
| | ||
| ch_for_mix.merged.mix(ch_for_mix.cadd) | ||
| ch_for_mix.vcfanno.mix(ch_for_mix.cadd) |
Contributor
There was a problem hiding this comment.
What are we mixing in ch_for_mix? 😄 Perhaps it could have another name.
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PR checklist
Fix issues missed in the previous 2 PRs.
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_singleton,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).