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Update UNIVERSC module #3485

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Update UNIVERSC module #3485

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@adamrtalbot adamrtalbot commented Jun 2, 2023 •
edited

  • Moves parameters from meta map to ext.args
  • Directs logs to stdout and stderr for proper handling by Nextflow
  • Catches if there are not 2 files (which would not work)
  • Removes modifications of containerOptions
  • FIxes bug where parameters were being added as an array (e.g. ["option"])
  • Updates tests to work with current test-datasets repo

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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [ ]

@adamrtalbot adamrtalbot closed this Jun 2, 2023
@adamrtalbot adamrtalbot reopened this Jun 2, 2023
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Should fix nf-core/scrnaseq#230

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Closed in favour of #3493

@adamrtalbot adamrtalbot closed this Jun 7, 2023
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