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port cnvkit/antitarget to nf-test and update cnvkit #5594

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merged 6 commits into from
May 13, 2024

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@famosab famosab commented May 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

Relates to #3937

@famosab famosab requested review from adamrtalbot, priesgo, SusiJo and a team as code owners May 13, 2024 11:11
@famosab famosab changed the title port cnvkit/antitarget to nf-test port cnvkit/antitarget to nf-test and update cnvkit May 13, 2024
@maxulysse maxulysse added this pull request to the merge queue May 13, 2024
Merged via the queue into nf-core:master with commit 7d8eff8 May 13, 2024
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@famosab famosab deleted the cnvkit-antitarget branch May 13, 2024 12:30
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