Group pipeline-Nextflow-* modules together for dependabot

[nwiltsie]

Description

This is an example of (hopefully) solving https://github.com/uclahs-cds/group-infrastructure/issues/79.

This changes the dependabot configuration to group updates from pipeline-Nextflow-config and pipeline-Nextflow-module into a single PR. That will allow us to test them both simultaneously, saving the need to test one, merge it, rebase the other, test it, and merge it.

I don't know if I have the syntax worked out correctly, but this needs to be merged before I can really test it. If it works as expected we should replicate this across all of our pipelines.

Testing Results

No pipeline changes.

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.

[yashpatel6]

Makes sense to me!

[nwiltsie]

Argh, I clearly didn't do this right: https://github.com/uclahs-cds/pipeline-recalibrate-BAM/network/updates/842195399

updater | 2024/06/14 22:50:16 INFO <job_842195399> Starting job processing
updater | 2024/06/14 22:50:16 WARN <job_842195399> Please check your configuration as there are groups where no dependencies match:
updater | - pipeline-submodules
updater | 
updater | This can happen if:
updater | - the group's 'pattern' rules are misspelled
updater | - your configuration's 'allow' rules do not permit any of the dependencies that match the group
updater | - the dependencies that match the group rules have been removed from your project
updater | 
updater | 2024/06/14 22:50:17 INFO <job_842195399> Starting grouped update job for uclahs-cds/pipeline-recalibrate-BAM
updater | 2024/06/14 22:50:17 INFO <job_842195399> Found 1 group(s).
updater | 2024/06/14 22:50:17 WARN <job_842195399> Skipping update group for 'pipeline-submodules' as it does not match any allowed dependencies.