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Add prefix to output file for barrnap

Open sofstam opened this issue 1 year ago • 2 comments

PR checklist

Updates barrnap module to include prefix in the output filename.

  • [ ] 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

sofstam avatar Jul 04 '24 07:07 sofstam

Hi! As you changed the name of the files produced by the module, the regression tests fail because they were not updated to the new names. In principle https://github.com/nf-core/modules/blob/master/tests/modules/nf-core/barrnap/test.yml should be updated, but I think that nf-core team members would love if the module were converted to the use of nf-test instead… https://nf-co.re/docs/tutorials/tests_and_test_data/nf-test_writing_tests

charles-plessy avatar Jul 04 '24 23:07 charles-plessy

Thank you, will update to nf-test.

sofstam avatar Jul 05 '24 01:07 sofstam