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Split validation to allow for streamlined parameter input #194

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merged 5 commits into from
Apr 29, 2024

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yashpatel6
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@yashpatel6 yashpatel6 commented Apr 26, 2024

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

  • 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
    metadata.yaml and 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.

Updating the parameter handling to:

  • Not require parameters for pipelines that are not selected to run
  • Validate parameters only for pipelines requested to run

Testing Results

NFTest with test-metapipeline-DNA-fastq-input ran successfully - /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-robust-validation/log-nftest-20240429T161625Z.log

  • Passes validation properly
    • Config: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-robust-validation/passes.config
    • Log: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-robust-validation/passes.log
  • Fails validation as expected
    • Config: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-robust-validation/fails.config
    • Log: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-robust-validation/fails.log

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@nwiltsie nwiltsie left a comment

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Looks great!

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@sorelfitzgibbon sorelfitzgibbon left a comment

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Great! Could the log also be changed to show which pipelines were selected?

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@kiarod kiarod left a comment

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Looks good Yash

@yashpatel6
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Great! Could the log also be changed to show which pipelines were selected?

Yep this will be included in the documentation overhaul PR I'll be making

@yashpatel6 yashpatel6 merged commit 820e663 into main Apr 29, 2024
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@yashpatel6 yashpatel6 deleted the yashpatel-robust-validation branch April 29, 2024 20:29
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4 participants