NFTest Manta was run with twice the default CPU and memory allocation and the run time was significantly reduced to 1m on A-mini sample indicating a successful integration of the base resource update feature. The same NFTest without any base resource updates had a runtime of 7m.
NFTest log:
without base resource update - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/dependabot/submodules/pipeline-submodules-897d4a3787/gsv_discovery-manta-std-input/call-gSV-5.1.0/HG002.N/log-call-gSV-5.1.0-20240617T182917Z/nextflow-log/trace.txt
with base resource update - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-add-base-resource-update/base-resource-update-std-input/call-gSV-5.1.0/HG002.N/log-call-gSV-5.1.0-20240628T235035Z/nextflow-log/trace.txt
[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.
[x] 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 run_delly = true, run_manta = true, run_qc = true. For run_delly = true, I have tested 'variant_type' set to gSV, gCNV, and both. The paths to the test config files and output directories are captured above in the Testing Results section.
Description
Add base resource update feature.
Closes #163
Testing Results
NFTest Manta was run with twice the default CPU and memory allocation and the run time was significantly reduced to
1mon A-mini sample indicating a successful integration of the base resource update feature. The same NFTest without any base resource updates had a runtime of7m.NFTest log:
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
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.[x] 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
run_delly = true,run_manta = true,run_qc = true. Forrun_delly = true, I have tested 'variant_type' set togSV,gCNV, and both. The paths to the test config files and output directories are captured above in the Testing Results section.