Add raredisease deepvariant reports to housekeeper bundle

[peterpru]

Description

This PR adds the deepvariant reports to the housekeeper bundle for the raredisease pipeline. To be tested at the same time as the corresponding hermes PR.

Closes: #4731

NB: To be deployed with the next release of RD (deepvar html file is now a mandatory file for hk, but the current RD version does not stage it for the store command to pick up yet).

Added

• deepvariant reports to the housekeeper bundle for the raredisease pipeline

Changed

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 raredisease-add-deepvariant-report-storing

• stage the necessary files:

• deploy the related hermes test branch: Add deepvariant-report to raredisease hermes#149

How to test

• Do cg workflow raredisease store amusingmarmoset

Expected test outcome

• Check that the command succeeds and the deepvar files are in the new hk bundle
• Take a screenshot and attach or copy/paste the output.

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 ...

[diitaz93]

👍

[sonarqubecloud]

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 SonarQube Cloud