sorelfitzgibbon commented 1 week ago

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.log

with panel of normals

config: /hot/code/sfitzgibbon/GitHub/uclahs-cds/pipeline-call-sSNV/test/config/untracked/a_mini-all-tools-pon.config yaml: /hot/code/sfitzgibbon/GitHub/uclahs-cds/pipeline-call-sSNV/test/yaml/a_mini_n2-std-input.yaml log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-fix-pon-check/slurm-230914.out

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 manifest block in the nextflow.config as part of this pull request; I 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.

github-actions[bot] commented 1 week ago

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:

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).
Manually: Follow these steps on Confluence.

sorelfitzgibbon commented 1 week ago

/fix-tests

github-actions[bot] commented 6 days ago

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with b03b04930551e35e83af4b8a214034451d35b17e. You must review my work before merging this pull request!