Add cg workflow nallo panel

[peterpru]

Description

This PR adds the generation of a Scout gene panel export and includes it in the cg workflow nallo config-case command.

For sysdev: the call to scout is the same as for raredisease, however, Nallo needs the gene panel information as a TSV file, and not as a bed file such as in raredisease/mip. Here the bed file is requested from scout, then the ## commented lines are removed, and the file is saved with the extension .tsv

Config-case triggers the gene panel command by having is_gene_panel_required set to True.

Added

• cg workflow nallo panel

Changed

• cg workflow nallo config-case triggers panel generation

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-nallo-gene-panel

How to test

• Do cg workflow nallo panel --help
• Do cg workflow nallo panel rightalpaca
• Delete the contents of the rightalpaca folder
• Do cg workflow nallo config-case rightalpaca

Expected test outcome

• Check that panel command is shown.

• Check that panel is generated and contents look as expected.

• After removing the contents of the analysis folder and triggering config-case, make sure that the file is generated correctly as part of the config-case command.

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]

Looks good!

[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

[peterpru]

stage deployed:

Production deployment: