Use methods.setup_process_afterscript() for process logs

[nwiltsie]

Description

This PR updates the pipeline to use the new setup_process_afterscript() method from uclahs-cds/pipeline-Nextflow-config#64.

Doing so allows us to get rid of a ton of boilerplate - specifically, the output: path(".command.*") directive and the corresponding publishDir directive on every process. Now the only required configuration is adding (e.g.) ext log_dir_suffix: { "-${sample_id}" } to every process that wants to customize the output log folder.

Testing Results

• NFTest
  • log: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/nwiltsie-streamlined-logging/log-nftest-20240603T210115Z.log
  • cases: default set

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 using NFTest, or I have justified why I did not need to run NFTest above.

[github-actions]

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["process","afterScript"]
+ {"1":"","2":"","3":"","closure":""}
@ ["process","ext"]
+ {"capture_logs":true,"commonAfterScript":{"1":"","2":"","3":"","closure":""},"log_dir":{"1":"ext","2":"ext","3":"ext","closure":"ext"}}

test/configtest-F32.json

@ ["process","afterScript"]
+ {"1":"","2":"","3":"","closure":""}
@ ["process","ext"]
+ {"capture_logs":true,"commonAfterScript":{"1":"","2":"","3":"","closure":""},"log_dir":{"1":"ext","2":"ext","3":"ext","closure":"ext"}}

If the above changes are surprising, stop and determine what happened.

If the above changes are expected, there are two ways to fix this:

1. Automatically: Post a comment starting with "/fix-tests" (without the quotes) and I will update the tests for you (you must review my work afterwards).
2. Manually: Follow these steps on Confluence.

[nwiltsie]

/fix-tests

[github-actions]

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with 328f39d. You must review my work before merging this pull request!

[yashpatel6]

Looks good!