This PR removes the methods.check_limits and methods.set_resources_allocation functions from config/methods.config in favor of the standardized versions from pipeline-Nextflow-config.
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[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 on at least one A-mini sample with aligner setting to BWA-MEM2, HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.
Description
This PR removes the
methods.check_limitsandmethods.set_resources_allocationfunctions fromconfig/methods.configin favor of the standardized versions from pipeline-Nextflow-config.Testing Results
NFTest results:
/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/nwiltsie_remove_duplicates/log-nftest-20240108T185912Z.logChecklist
[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 the branch protection rule following the github standards before opening this pull request, or the branch protection rule has already been set up.
[x] I have added my name to the contributors listings in the
manifestblock in thenextflow.configas 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.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.)[x] I have tested the pipeline on at least one A-mini sample with aligner setting to
BWA-MEM2,HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.