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Add prefix to output file for barrnap #5919

Merged
merged 15 commits into from
Jul 11, 2024
Merged

Add prefix to output file for barrnap #5919

merged 15 commits into from
Jul 11, 2024

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sofstam
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@sofstam sofstam commented Jul 4, 2024

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 sofstam requested a review from danilodileo as a code owner July 4, 2024 07:26
@charles-plessy
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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

@sofstam sofstam marked this pull request as draft July 5, 2024 01:01
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sofstam commented Jul 5, 2024

Thank you, will update to nf-test.

@sofstam sofstam marked this pull request as ready for review July 9, 2024 06:59
@sofstam sofstam requested a review from a team as a code owner July 9, 2024 06:59
@sofstam sofstam requested review from Aratz and removed request for a team July 9, 2024 06:59
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@sofstam sofstam requested a review from SPPearce July 10, 2024 02:40
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Ok, good to go now.

@sofstam sofstam added this pull request to the merge queue Jul 11, 2024
Merged via the queue into nf-core:master with commit c4c7ecb Jul 11, 2024
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@sofstam sofstam deleted the barrnap branch July 11, 2024 01:02
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3 participants