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Align parabricks subworkflow #6876

Merged
merged 80 commits into from
Feb 18, 2025
Merged

Align parabricks subworkflow #6876

merged 80 commits into from
Feb 18, 2025

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famosab
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@famosab famosab commented Oct 28, 2024

PR checklist

Closes #6894

  • 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

@famosab famosab linked an issue Oct 29, 2024 that may be closed by this pull request
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famosab commented Feb 17, 2025

Now it should work.

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Revert the changes to the config and I think we're good for a merge

@famosab famosab enabled auto-merge February 18, 2025 14:15
@famosab famosab added ready to merge and removed help wanted Extra attention is needed labels Feb 18, 2025
@famosab famosab added this pull request to the merge queue Feb 18, 2025
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Feb 18, 2025
@famosab famosab added this pull request to the merge queue Feb 18, 2025
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famosab commented Feb 18, 2025

The problem is that sometimes the GPUs are not really accessible and then the PR is removed from the merge queue again :(

@famosab famosab removed this pull request from the merge queue due to a manual request Feb 18, 2025
@famosab famosab added this pull request to the merge queue Feb 18, 2025
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Feb 18, 2025
@famosab famosab added this pull request to the merge queue Feb 18, 2025
Merged via the queue into nf-core:master with commit 205d830 Feb 18, 2025
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@famosab famosab deleted the parabricks-sbwf branch February 18, 2025 15:46
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new subworkflow: fastq_align_parabricks
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