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More module updates again #6812

Merged
merged 10 commits into from
Oct 21, 2024
Merged

More module updates again #6812

merged 10 commits into from
Oct 21, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Oct 20, 2024

Just a bunch of regular modules updates, mostly for getting versions of upstreas stuff with ARM builds available,

Only slightly unusual thing is the use of Seqera Containers on cat/fastq. I've done that to match the container to the coreutils version. The newer coreutils conda package will give us ARM compatibility, but the previous ubuntu container will have a different version, and with Seqera Containers we can match it properly.

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

@pinin4fjords pinin4fjords mentioned this pull request Oct 20, 2024
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@maxulysse maxulysse added this pull request to the merge queue Oct 21, 2024
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Only slightly unusual thing is the use of Seqera Containers on cat/fastq. I've done that to match the container to the coreutils version. The newer coreutils conda package will give us ARM compatibility, but the previous ubuntu container will have a different version, and with Seqera Containers we can match it properly.

#5968

@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Oct 21, 2024
@pinin4fjords pinin4fjords added this pull request to the merge queue Oct 21, 2024
@maxulysse maxulysse removed this pull request from the merge queue due to a manual request Oct 21, 2024
@maxulysse maxulysse merged commit a1abf90 into master Oct 21, 2024
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@maxulysse maxulysse deleted the more_module_updates2 branch October 21, 2024 09:31
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3 participants