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port parabricks/haplotypecaller to nf-test and update #7468

Merged
merged 19 commits into from
Feb 20, 2025
Merged

port parabricks/haplotypecaller to nf-test and update #7468

merged 19 commits into from
Feb 20, 2025
+398 −148

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famosab
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@famosab famosab commented Feb 11, 2025 •
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PR checklist

Closes #XXX
Continues #6976

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@famosab famosab requested a review from a team as a code owner February 11, 2025 14:51
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@famosab famosab added the help wanted Extra attention is needed label Feb 12, 2025
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famosab commented Feb 18, 2025
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@famosab famosab added Ready for Review gpu module uses GPU and removed help wanted Extra attention is needed labels Feb 20, 2025
@famosab famosab enabled auto-merge February 20, 2025 13:17
maxulysse
maxulysse reviewed Feb 20, 2025
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modules/nf-core/parabricks/haplotypecaller/main.nf
Comment on lines +14 to +15
tuple val(meta), path("*.vcf"), optional: true, emit: vcf
tuple val(meta), path("*.g.vcf.gz"), optional: true, emit: gvcf
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so vcf or g.vcf.gz, no vcf.gz?

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yeah not supported by parabricks - I already asked on slack to add bgzip to the next container

maxulysse
maxulysse reviewed Feb 20, 2025
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Minor comments

@famosab famosab added this pull request to the merge queue Feb 20, 2025
Merged via the queue into nf-core:master with commit 0a364de Feb 20, 2025
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@famosab famosab deleted the hc branch February 20, 2025 13:51
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