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fix special characters in samtools/view container #7036

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merged 2 commits into from
Nov 20, 2024

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tkchafin
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There were some weird non-printing characters in the Docker container name for samtools/view which caused a failure when running using Docker due to the name failing to resolve.

samtools/view also uses a different container than the rest of the samtools modules, but I've left that unchanged here

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

@SPPearce SPPearce enabled auto-merge November 20, 2024 12:11
@SPPearce
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Ok, thanks!
If you ask on the nf-core slack #github-invitations channel you can get added to the organisation for the tests to automatically run.

@SPPearce SPPearce added this pull request to the merge queue Nov 20, 2024
Merged via the queue into nf-core:master with commit 64eef62 Nov 20, 2024
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2 participants