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checkm/qa: Improve input validation #7119

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merged 2 commits into from
Dec 1, 2024

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@dialvarezs dialvarezs commented Nov 28, 2024

This PR improves the validation of the input coverage_file to handle cases where .isFile() is not defined, for example an empty list ([]).

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

@dialvarezs dialvarezs changed the title checkm/qa: Improve input condition checkm/qa: Improve input validation Nov 28, 2024
@dialvarezs dialvarezs enabled auto-merge November 28, 2024 16:27
@dialvarezs dialvarezs mentioned this pull request Nov 28, 2024
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@dialvarezs dialvarezs added this pull request to the merge queue Dec 1, 2024
@sateeshperi sateeshperi removed this pull request from the merge queue due to a manual request Dec 1, 2024
@sateeshperi sateeshperi enabled auto-merge December 1, 2024 07:20
@sateeshperi sateeshperi added this pull request to the merge queue Dec 1, 2024
Merged via the queue into nf-core:master with commit 867961a Dec 1, 2024
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LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
Improve input condition

Co-authored-by: Sateesh_Peri <[email protected]>
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2 participants