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SHAPEIT5_SWITCH Migrate to nf-test #7066

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SHAPEIT5_SWITCH Migrate to nf-test #7066

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LouisLeNezet
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PR checklist

Migration to nf-test for SHAPEIT5_SWITCH process.
Modified stub and update shapeit5 version to 5.1.1

  • 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

@LouisLeNezet LouisLeNezet requested a review from a team as a code owner November 22, 2024 18:06
SPPearce
SPPearce reviewed Nov 25, 2024
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modules/nf-core/shapeit5/switch/tests/main.nf.test
Comment on lines +55 to +56
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf",checkIfExists:true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi",checkIfExists:true)
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Can we please do something with this dataset on the test-data repository, rather than leave it in the delete_me folder? You've got multiple modules here using it.

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You're totally right.
I'll discuss it in the dedicated slack channel and update this pull request when done !

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Those files are also present on the phaseimpute branch of the test-datasets repository.
Should I use these files ?

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@LouisLeNezet @SPPearce