add panel of normals

[zhuchcn]

Description

Add panel_of_normals_vcf to MuTect2.

There is a PON included in the GATK best practice resource bundle (see here for more information), which was created from 1K genome WGS. CCLE's initial analysis used MuTect1, and a PON that they created from ~8000 TCGA normals and filtered using their own algorithm (not confirmed but my guess is MuTect1 doesn't support PON). But in their latest release (23Q4), CCLE switched to using MuTect2 and also this 1K genome PON from GATK. With the addition of PON, 3000 - 7000 SNVs were filtered out, and the results of our pipeline aligned well with CCLE's latest release.

Closes #...

Testing Results

• Tumor/Normal Paired Sample:
  • sample:
  • input YAML:
  • config:
  • output:
• Tumor-only Sample:
  • sample:
  • input YAML:
  • config:
  • output:
• Multi-tumor Sample:
  • sample:
  • input YAML:
  • config:
  • output:

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.

• [ ] 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.

• [ ] 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 on at least one A-mini sample.

[zhuchcn]

Yeah, the pipeline output of the 6 cell lines with the use of PON are here: /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/CCLE/processed/WXS/PON_1KG/metapipeline-submit-pipeline-0.1.0/main_workflow/call-sSNV-8.0.0

For CCLE's SNV:

• 22Q1: /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/CCLE/raw_data/mutation/CCLE_fusions_22Q1.csv
• 23Q4: /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/CCLE/raw_data/mutation/OmicsSomaticMutations_23Q4.csv

[tyamaguchi-ucla]

Anything else to add @yashpatel6 ?