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Replace ubuntu for all modules using it - meta PR #7215

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merged 17 commits into from
Dec 13, 2024

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maxulysse
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@maxulysse maxulysse commented Dec 13, 2024

docker: https://wave.seqera.io/view/builds/bd-838ba80435a629f8_1
singularity: https://wave.seqera.io/view/builds/bd-2f90c612c8e49f19_1

modules left in this PR are:

  • cat/fastq
  • custom/tabulartogseacls
  • custom/tabulartogseagct
  • igv/js
  • md5sum
  • shasum

Other modules have been split out:

Conda in Pytest has been fixed in #7219

PR checklist

Closes #5968

  • 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

@maxulysse maxulysse requested a review from a team as a code owner December 13, 2024 11:16
maxulysse added a commit to maxulysse/nf-core_modules that referenced this pull request Dec 13, 2024
@maxulysse maxulysse mentioned this pull request Dec 13, 2024
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github-merge-queue bot pushed a commit that referenced this pull request Dec 13, 2024
fix conda pytests cf #7215
@maxulysse maxulysse changed the title Replace ubuntu for all modules using it Replace ubuntu for all modules using it - meta PR Dec 13, 2024
maxulysse added a commit to maxulysse/nf-core_modules that referenced this pull request Dec 13, 2024
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@edmundmiller edmundmiller left a comment

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LGTM!

Should probably bump up the docs, I think they say somewhere to use ubuntu as a base.

@maxulysse maxulysse added this pull request to the merge queue Dec 13, 2024
Merged via the queue into nf-core:master with commit a57fc22 Dec 13, 2024
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@maxulysse maxulysse deleted the unify_5968 branch December 13, 2024 22:37
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[FEATURE] Centralize all modules using ubuntu container into a single container
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