Add conditional parameters for tomte

[fevac]

Description

Added

• Conditional parameters for tomte: gene panel, genome and tissue

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-servers-stage.sh tomte_conditional_config
  
  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b tomte_update_params -a

How to test

• cg workflow tomte config-case CASE.
  • Make sure it creates a gene panel file called gene_panels.bed that is not empty and formatted as expected

• Make sure that _nextflow_config.json contains the following parameters set params.gene_panel_clinical_filter params.tissue params.genome

• cg workflow tomte start CASE. Starts as expected without errors.

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 ...

[fevac]

Pending to revise in a different PR:

• get_aggregated_panels: has a weird behaviour. Make it clear and add documentation.
• get source for external and downsampled cases

[diitaz93]

my concerns have been addressed 👍

[ivadym]

Nothing more from my part, great job! 🏁 🏎️

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[fevac]

tests are passing

[fevac]

Note

This branch as not been deployed in production due to issues with Hasta