add raredisease pedigree check

[peterpru]

Description

The RareDisease requires an additional metric from the multiQC data file with respect to the other Nextflow pipelines, which is the pedigree check. This is a pair-wise sample metric, meaning there is a value for every pair of samples combination in the case. To parse them, the method get_multiqc_json_metrics from NfAnalysisAPI is overridden in RarediseaseAnalysisAPI.

Added

• Pedigree check in raredisease QC: parent_error_ped_check

Changed

• MEDIAN_TARGET_COVERAGE threshold to >25

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-pedigree-check

How to test

• Do nano /home/proj/stage/analysis/cases/funkitten/multiqc/multiqc_data/multiqc_data.json and MEDIAN_TARGET_COVERAGE set to 26 for all three samples

• Do cg workflow raredisease metrics-deliver funkitten with MEDIAN_TARGET_COVERAGE set to 26.

• Do sed -i 's/"parent_error_ped_check": "False",/"parent_error_ped_check": "True",/g' /home/proj/stage/analysis/cases/funkitten/multiqc/multiqc_data/multiqc_data.json

• Do cg workflow raredisease metrics-deliver funkitten

Expected test outcome

• Check that there are no errors, and command completes as expected.
  

• When setting parent error to True, the command should fail. Error needs to be propagated to trailblazer
  

• See that the check is visible in the deliverables.yaml file:
  

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 ...

[islean]

Looks good! A bit confused over certain parts of the code.

[peterpru]

Thank you all for your comments @ChrOertlin, @islean, after multiple discussions with @diitaz93 and @jemten we have decided to keep the code as is, and add test functions to make sure it works as intended. I have marked most conversations as resolved. We can refactor the nextflow QC code in the future, or turn it into a microservice where we have it outside of cg.

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[diitaz93]

Looks good 🚀

[peterpru]

Successfully deployed in stage:

Deployed in production: