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port parabricks/genotypegvcf to nf-test #6980

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merged 14 commits into from
Dec 10, 2024
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famosab
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@famosab famosab commented Nov 13, 2024

PR checklist

Closes #XXX

  • 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 November 13, 2024 11:13
@famosab famosab requested a review from mirpedrol November 13, 2024 11:13
@famosab famosab added gpu module uses GPU nf-test labels Nov 18, 2024
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famosab commented Dec 2, 2024

Now only conda seems to fail but that is expected because the tool is not available on conda.

@mashehu
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mashehu commented Dec 2, 2024

Can you please add the module with conda to the exclusion criteria?

@famosab famosab added this pull request to the merge queue Dec 10, 2024
Merged via the queue into nf-core:master with commit 51145aa Dec 10, 2024
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@famosab famosab deleted the genotypegvcf branch December 10, 2024 07:13
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4 participants