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Fix badly named variable #6763

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merged 1 commit into from
Oct 10, 2024
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pinin4fjords
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Fixing an error reported in nf-core/rnaseq#1390, caused by a mistake in variable naming.

PR checklist

Closes #XXX

  • 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

@pinin4fjords pinin4fjords added this pull request to the merge queue Oct 10, 2024
Merged via the queue into master with commit aef0e74 Oct 10, 2024
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@pinin4fjords pinin4fjords deleted the rnaseq_prepro_variable_name_fix branch October 10, 2024 10:06
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@maxulysse @SPPearce For some reason the singularity test was hanging here, on SALMON_QUANT. I cancelled it and it went through. The same happened in the merge queue.

I have no reason to think that anything in this change would have triggered that (it's trivial), but maybe a problem has developed in the CI, which we should look out for.

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Yes, we seem to have a general issue with pulling singularity containers at the moment

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3 participants