Pcgr v2.2.5

[qclayssen]

bump pcgr v2.2.1 -> v2.2.5

[Copilot]

Pull Request Overview

This PR updates the PCGR (Personal Cancer Genome Reporter) version from v2.2.1 to v2.2.5. The update includes corresponding changes to VEP annotation fields to support new gnomAD genome frequency annotations.

• Updated Docker conda environment lock files to reference PCGR v2.2.5
• Added gnomAD genome (gnomADg) annotation fields to VEP CSQ format strings
• Added logging imports and logger initialization to several workflow modules

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
docker/Dockerfile.pcgr	Updated conda lock file URLs from PCGR v2.2.1 to v2.2.5 for both pcgr and pcgrr environments
bolt/common/constants.py	Extended VEP CSQ format strings to include gnomAD genome frequency fields (gnomADg_*)
bolt/workflows/smlv_somatic/report.py	Added logging module import and logger initialization; defined pcgr_output_dir variable
bolt/workflows/smlv_germline/report.py	Added logging module import and logger initialization
bolt/workflows/smlv_somatic/filter.py	Added duplicate logging import
bolt/workflows/other/cancer_report.py	Added logging module import

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