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Added nf-tests to gprofile2/gost #7265

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merged 9 commits into from
Jan 15, 2025
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nschcolnicov
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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 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

@SPPearce
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SPPearce commented Jan 8, 2025

Can you remove the pytest files please.

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Looks generally fine, but needs pytest removing and conda fixing.

@nschcolnicov nschcolnicov requested a review from a team as a code owner January 9, 2025 17:25
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@SPPearce SPPearce left a comment

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Looks good to me.

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SPPearce commented Jan 10, 2025

Oh, I guess that we should be using testdata from the modules test data branch. Any chance you are willing to copy them over from differential abundance? Same goes for the other modules.

@nschcolnicov
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@SPPearce I created a PR for all of the datasets across all of my current open modules PRs:
nf-core/test-datasets#1456

@SPPearce SPPearce enabled auto-merge January 15, 2025 09:45
@SPPearce SPPearce added this pull request to the merge queue Jan 15, 2025
Merged via the queue into master with commit 135782a Jan 15, 2025
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@SPPearce SPPearce deleted the add_nftests_gprofiler2_gost branch January 15, 2025 09:48
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2 participants