WIP: Fix warning nf core lint and nextflow lint #1955
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tests warnings: 258 -> 129 |
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maxulysse
commented
Aug 18, 2025
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solving conflicts locally, as there's a complex snapshot merge conflict involved |
famosab
reviewed
Aug 21, 2025
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famosab
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A few general points:
- does not need to be fixed here but I think we should be more consistent in the code commenting (stuff like channel: [...])
- I am not a fan of just adding a _ after the name like
bam_to suppress the warning. I would go for something more descriptive likebam_fileor change the channel name toch_bamto get rid of the warning. - I noticed some changes in the snaps that I did not expect (like more processes being run), maybe we can address those? (I did not comment where I just saw that versions were being recovered :)
Note:
- I did not review the nf-core modules, will check for the versions though after submitting this review.
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| - [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Pipeline Test Warnings | ||
| - [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Subworkflow Test Warnings |
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Why do you split this here in the Changelog?
Suggested change
| - [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Pipeline Test Warnings | |
| - [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Subworkflow Test Warnings | |
| - [1955](https://github.com/nf-core/sarek/pull/1955) - Fix nf-core/tools lint Pipeline and Subworkflow Test Warnings |
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Note to myself to check this in the end again
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Do we have nf-test tests for the local modules or do we not do that because they are quite simple? Just wondering.
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| touch ${meta.id}.reindex.bam | ||
| touch ${meta.id}.reindex.bam.bai |
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| genotype_index // channel: [ val(meta), [ tbi ] ] | ||
| genotype_vcf // channel: [ val(meta), [ vcf ] ] |
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Suggested change
| genotype_index // channel: [ val(meta), [ tbi ] ] | |
| genotype_vcf // channel: [ val(meta), [ vcf ] ] | |
| genotype_index // channel: [ meta, tbi ] | |
| genotype_vcf // channel: [ meta, vcf ] |
or are these multiple vcfs / tbis?
| "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools false": { | ||
| "content": [ | ||
| 9, | ||
| 12, |
| "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools false": { | ||
| "content": [ | ||
| 7, | ||
| 10, |
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| "INDEX_CRAM": { | ||
| "samtools": 1.21 | ||
| }, | ||
| "MOSDEPTH": { | ||
| "mosdepth": "0.3.10" | ||
| }, | ||
| "SAMTOOLS_STATS": { | ||
| "samtools": 1.21 | ||
| }, |
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Are these here on purpose?
| @@ -1,26 +1,26 @@ | |||
| { | |||
| "-profile test --tools cnvkit --input recalibrated.csv --only_paired_variant_calling": { | |||
| "-profile test --tools cnvkit --input recalibrated_somatic.csv": { | |||
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Can we change the order again to make the snapshots comparable on review?
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Replaces fully #1911
Overlaps a bit with #1912
Splitting this beast in:
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).