add raredisease to cli cg workflow

[peterpru]

Description

This PR aims to add raredisease as a cli option in cg workflow. This is a redo of PR #2592, which failed on deployment and was reverted in #2646. The code in this PR is the same as in the first PR.

Added

• cli option raredisease for cg workflow

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 add-raredisease-to-workflow -a

How to test

• Do cg workflow --help

Expected test outcome

• cg workflow shows the new option:

• Check that installing on stage shows that the alembic revision is installed correctly.
• When completing the tests, pull master and show that the alembic downgrade completed successfully.

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 ...

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[seallard]

💪

[peterpru]

Successfully installed on stage:

[peterpru]

Thank you very much for the help @seallard :

Deployed in prod: