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Add new standard workflows for pipeline #52

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merged 3 commits into from
Mar 7, 2024
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@nwiltsie nwiltsie commented Mar 6, 2024

Description

This adds two new standard workflows to this pipeline:

  1. The new Nextflow configuration regression test Action from Create usable Nextflow regression test Action tool-Nextflow-action#16. I have not added any actual tests yet (there aren't any NFTest cases so I couldn't copy them over!).
  2. The new documentation Action from Update documentation script to correctly handle versions tool-Nextflow-action#13.

For the documentation workflow, nothing should happen until this PR is merged, and then the documentation should be updated automatically on every update to main and every tag creation. After that is done I will go back and backfill docs for the two existing releases.

Checklist

  • I have read the code review guidelines and the code review best practice on GitHub check-list.

  • I have reviewed the Nextflow pipeline standards.

  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

  • I have set up or verified the branch protection rule following the github standards before opening this pull request.

  • I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

  • I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

  • I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

  • I have tested the pipeline on at least one A-mini sample.

@nwiltsie nwiltsie requested a review from a team March 6, 2024 17:51
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nwiltsie commented Mar 6, 2024

Interesting, the Nextflow Tests workflow complained that no jobs were found. For the time being I've disabled the workflow manually, but we should re-enable it once tests are added or we make the shared workflow robust to this (common) case.

Screenshot 2024-03-06 at 9 55 07 AM

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@yashpatel6 yashpatel6 left a comment

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Agreed, it'll be fairly common to not have test cases initially

@nwiltsie nwiltsie merged commit c9b94ff into main Mar 7, 2024
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@nwiltsie nwiltsie deleted the nwiltsie-add-new-actions branch March 7, 2024 21:57
@alkaZeltser alkaZeltser mentioned this pull request Mar 7, 2024
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2 participants