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add storing of parameters #312

Merged
merged 2 commits into from
Oct 25, 2024
Merged

add storing of parameters #312

merged 2 commits into from
Oct 25, 2024

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sorelfitzgibbon
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Description

Uses the new store_object_as_json method from uclahs-cds/pipeline-Nextflow-config#43 to store the pipeline's parameters in ${params.log_output_dir}/nextflow-log/params.json.

The parameters from my test run were successfully saved to:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-store-parameters/a_mini-all-tools-std-input/call-sSNV-8.1.0/S2-v1.1.5/log-call-sSNV-8.1.0-20241010T194927Z/nextflow-log/params.json

Closes #307

Testing Results

NFTest
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-store-parameters/log-nftest-20241010T194919Z.log
cases: a_mini-all-tools-std-inpu

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; I 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.

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@j2salmingo j2salmingo left a comment

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lgtm

@sorelfitzgibbon sorelfitzgibbon merged commit 0835f91 into main Oct 25, 2024
8 checks passed
@sorelfitzgibbon sorelfitzgibbon deleted the sfitz-store-parameters branch October 25, 2024 23:35
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Use store_object_as_json to store parameters
2 participants