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Bump samtools to v18 #4432

Merged
merged 71 commits into from
Dec 5, 2023
Merged

Bump samtools to v18 #4432

merged 71 commits into from
Dec 5, 2023

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nvnieuwk
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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:
    • 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

@nvnieuwk
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nvnieuwk commented Dec 4, 2023

@FriederikeHanssen @mashehu This one should now finally be ready, can you take a look (I'm sorry for how big this became, had to rewrite half the tests 😢)

@SPPearce
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SPPearce commented Dec 5, 2023

I think those leftover build files are breaking pytest in general.

@nvnieuwk
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nvnieuwk commented Dec 5, 2023

I think those leftover build files are breaking pytest in general.

Oh that's bad :o

@mashehu mashehu added this pull request to the merge queue Dec 5, 2023
@nvnieuwk
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nvnieuwk commented Dec 5, 2023

@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Dec 5, 2023
@nvnieuwk nvnieuwk added this pull request to the merge queue Dec 5, 2023
Merged via the queue into nf-core:master with commit a64788f Dec 5, 2023
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@nvnieuwk nvnieuwk deleted the bump-samtools branch December 5, 2023 22:56
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5 participants