fix check for panel of normals and add in log #319
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sorelfitzgibbon
requested review from
tyamaguchi-ucla,
yashpatel6,
maotian06 and
a team
as code owners
yashpatel6
approved these changes
Oct 25, 2024
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Bleep bloop, I am a robot. Alas, some of the Nextflow configuration tests failed! test/configtest-F16.json@ ["params","panel_of_normals_vcf"]
+ ""test/configtest-F32.json@ ["params","panel_of_normals_vcf"]
+ ""If the above changes are surprising, stop and determine what happened. If the above changes are expected, there are two ways to fix this:
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/fix-tests |
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Bleep bloop, I am a robot. I have updated all of the failing tests for you with b03b049. You must review my work before merging this pull request! |
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Description
Running without a panel of normals was triggering a warning. This fixes that and adds the specified panel of normals to the Mutect2 log output.
Closes #308
Testing Results
without panel of normals
NFTest a_mini-all-tools-std-input
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-fix-pon-check/log-nftest-20241025T230650Z.logwith panel of normals
config:
/hot/code/sfitzgibbon/GitHub/uclahs-cds/pipeline-call-sSNV/test/config/untracked/a_mini-all-tools-pon.configyaml:
/hot/code/sfitzgibbon/GitHub/uclahs-cds/pipeline-call-sSNV/test/yaml/a_mini_n2-std-input.yamllog:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-fix-pon-check/slurm-230914.outChecklist
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
manifestblock in thenextflow.configas part of this pull request; I 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.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.)I have tested the pipeline on at least one A-mini sample.