Fix linting and local sbwf#293
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atrigila
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atrigila
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Mostly good, just one question
| // Prepare reference genome files | ||
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| include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx' |
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I agree that it doesn't check the nf-core guidelines as a sbwf.
However, I would argue that these guidelines are meant for the nf-core/modules repository, to avoid bloating the repo with trivial sbwf. I think that for local sbwf this constraint is maybe not relevant, as this allow to properly isolate and test channel handling while reducing the length of huge main.nf file.
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I don't understand the decision of having a prepare_genome subworkflow. What was the issue before with how things were done? Thanks.
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This was a recommendation from Maxime to take out the genome indexing out of the local phaseimpute utils sbwf.
I agree that the sbwf is a bit trivial, but the "complex" channel handling make it fit from my point of view as a local sbwf.
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Hi @atrigila, |
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PR checklist
In this PR, I fixed some small issues present in local subworkflows.
I've updated the documentation and added new tests.
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).