Add GENS upload for TGA

[mathiasbio]

Description

GENS has previously only been activated for WGS in Balsamic, however with the inclusion of this PR into production Clinical-Genomics/BALSAMIC#1448 CNV and BAF profiles from TGA samples can be uploaded as well. This feature is planned for release 16.0.0 of Balsamic (somewhere around August maybe) and requires a couple of small changes in CG.

Added

• gnomad-af argument to TGA samples

Changed

• gens upload no longer filters out TGA samples

Fixed

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

• Store a TGA case that has been run on balsamic pr: feat: merge vardict and tnscope BALSAMIC#1475
• Run cg upload and ensure that the GENS files are uploaded! https://gens-stage.scilifelab.se/2022-36079-31?region=X:62040080-155262060&variant=7514985b8fbc6be5d880fc5e318769d7&genome_build=37&case_id=sureroughy&individual_id=ACC10867A1
• Run CG start on a TGA case and ensure that GENS arguments are provided

Expected test outcome

• Check that GENS files for TGA cases are now uploaded to GENS
• Ensure that TGA case can be started with GENS arguments
• Take a screenshot and attach or copy/paste the output. (See gnomad specific argument --gnomad-min-af5 , it is also picking up the new PON version)

• Ensure that WGS case can STILL be started with GENS arguments

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud