Use store_object_as_json method to store parameters #47
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nwiltsie
requested review from
tyamaguchi-ucla,
yashpatel6 and
Faizal-Eeman
as code owners
|
Would it make sense for the JSON to be saved under |
Yeah that seems fair! I'll update it. |
|
Okay, after bd3485b the params file is now saved under
(I canceled that job almost immediately but the file was still produced correctly.) |
yashpatel6
approved these changes
Dec 22, 2023
This was referenced Aug 12, 2024
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Description
This just makes use of the new
store_object_as_jsonmethod from uclahs-cds/pipeline-Nextflow-config#43 to store the pipeline's parameters in${params.log_output_dir}/params.json.The parameters from my test run were successfully saved to
/hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/nwiltsie_log_params/A-mini-n2/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/log-recalibrate-BAM-1.0.0-rc.4-20231222T191057Z/params.json.Testing Results
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
manifestblock in thenextflow.configas part of this pull request, am listedalready, or do not wish to be listed. (This acknowledgement is optional.)
I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile 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 using NFTest, or I have justified why I did not need to run NFTest above.