Added method get_managed_variants to mip rna workflow

[diitaz93]

Description

The MipRNAAnalysisAPI didn't have a get_managed_variants method which raised an error when running cg workflow mip-rna start -sa star_fusion hugewasp

Added

• Method get_managed_variants to MipRNAAnalysisAPI

Changed

• Moved method write_managed_variants from MipDNAAnalysisAPI to MipAnalysisAPI so that it is available also for MipRNA

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

• Do ...

Expected test outcome

• Check that ...
• 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 ...

[peterpru]

I am not a code owner, so you might need sysdev 💯

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[ivadym]

👍 🔥 ⚡

[diitaz93]

Deployed to stage:

Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/proj/stage/flow_cells/180509_D00450_0598_BHGYFNBCX2
done.
Log deploy... done.
cg, version 54.2.1
θ61° 3d [js.diazboada@hasta:

Deployed to production:

Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/proj/stage/flow_cells/180509_D00450_0598_BHGYFNBCX2
done.
Log deploy... done.
cg, version 54.2.1
θ61° 3d [js.diazboada@hasta: