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Add fallback to Download Pipeline Workflow #2846

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merged 3 commits into from
Mar 14, 2024

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MatthiasZepper
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@MatthiasZepper MatthiasZepper commented Mar 13, 2024

  • Apparently, not all nf-core pipelines fully support stub runs. Since the download_pipeline.yml GitHub Actions workflow tested the pipeline in -stub/-stub-run mode, this test failed on some pipeline repositories. With this update, the workflow will still attempt running the downloaded pipeline with the -stub option first, but if that fails, it tries to run the pipeline without the -stub option. Mind that any step failure will trigger the regular run, whether it is related to the -stub parameter or not.

  • Additionally, I have added the edited and synchronized types to the event trigger, so the test is automatically rerun, if further changes to dev are made while the PR to master is open.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated

@MatthiasZepper
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See tests for the modified workflow on my fork of the bamtofastq pipeline.

  • In the initial version, the fallback worked, but the whole job (test) would nonetheless be considered a failure due to the one failing step.
  • Then I added a continue-on-error: true to the stub run, which allowed the whole job to finish successfully despite failure, but the fallback step was also not triggered.
  • Hence, I also modified the if: condition of the fallback, so it will run despite the continue-on-error: true, which sets the step's conclusion to success despite exit 1.

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@mirpedrol mirpedrol left a comment

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LGTM, thanks!

@MatthiasZepper MatthiasZepper merged commit 3fe0a1f into nf-core:dev Mar 14, 2024
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@MatthiasZepper MatthiasZepper deleted the DownloadAction-FixStub branch March 14, 2024 11:45
@edmundmiller edmundmiller added the download nf-core download label Jun 13, 2024
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3 participants