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Run snv-annotation in parallel #261

Merged
merged 2 commits into from
Jul 23, 2024
Merged

Run snv-annotation in parallel #261

merged 2 commits into from
Jul 23, 2024

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fellen31
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@fellen31 fellen31 commented Jul 22, 2024 •
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This PR closes #203 by moving concatenation of multisample VCFs from within short_variant_calling to nallo.nf, after SNV annotation but before ranking.

There are now 3 available SNV outputs: *_snv.vcf.gz, *_snv_annotated.vcf.gz, or *_snv_annotated_ranked.vcf.gz that are published in results/snvs/{single_sample,multi_sample}/${sample} depending on whether annotation and ranking is active.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 22, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 14003fa

+| ✅ 160 tests passed       |+
#| ❔  17 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 10:23:48

@fellen31 fellen31 force-pushed the parallel-vep branch 19 times, most recently from b9062cf to 8edd8df Compare July 22, 2024 15:40
@fellen31 fellen31 marked this pull request as ready for review July 22, 2024 15:55
@fellen31 fellen31 requested a review from a team as a code owner July 22, 2024 15:55
@fellen31 fellen31 mentioned this pull request Jul 22, 2024
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Lucpen
Lucpen reviewed Jul 23, 2024
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Super nice! Just one question, do you know what the consensus for the ifs and skips are? It would be good to double check if they should be within the subworkflows or in the configs.

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fellen31 commented Jul 23, 2024 •
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Super nice! Just one question, do you know what the consensus for the ifs and skips are? It would be good to double check if they should be within the subworkflows or in the configs.

I think leaning towards subworkflows, and I think that was Anders opinion as well (though not 100% sure). Even though it's a bit ugly I think it makes it more clear than having to go to back and forth to the configs and check.

I do have ext.when for one process in rank_variants.config and for one process in prepare_genome.config, which I could change to params.skip... in another PR to make it consistent. The rest should only be param.skip...'s in workflows/nallo.nf.

Lucpen
Lucpen approved these changes Jul 23, 2024
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LGTM!

@fellen31 fellen31 merged commit 0fabd11 into genomic-medicine-sweden:dev Jul 23, 2024
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@fellen31 fellen31 deleted the parallel-vep branch July 23, 2024 11:23
@fellen31 fellen31 mentioned this pull request Aug 15, 2024
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Move SNV concatenation from short_variant_calling to after annotation
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@fellen31 @Lucpen