Use store_object_as_json method to store parameters

[nwiltsie]

Description

This just makes use of the new store_object_as_json method from https://github.com/uclahs-cds/pipeline-Nextflow-config/pull/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

• NFTest
  • log: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/nwiltsie_log_params/log-nftest-20231222T191047Z.log
  • cases: default set

Checklist

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

• [x] I have reviewed the Nextflow pipeline standards.

• [x] 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].

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

• [x] 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.)

• [x] 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.)

• [x] I have tested the pipeline using NFTest, or I have justified why I did not need to run NFTest above.

[yashpatel6]

Would it make sense for the JSON to be saved under log-.../nextflow-log/?

[nwiltsie]

Would it make sense for the JSON to be saved under log-.../nextflow-log/?

Yeah that seems fair! I'll update it.

[nwiltsie]

Okay, after bd3485b the params file is now saved under nextflow-log/:

/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.4-20231222T194513Z/nextflow-log/params.json

(I canceled that job almost immediately but the file was still produced correctly.)