Raredisease add QC check for contamination and adapters

[peterpru]

Description

This PR aims to add a QC check for adapter content and sample contamination.

For the reviewer, adapter content is calculated using a 0.005 fraction of bases as cutoff (0.5%), using read length and the number of sequenced reads for a sample. Sample contamination is retrieved from haplocheck output, where the result is YES or NO.

Added

• Raredisease QC check adapter content
• Raredisease QC check sample contamination

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 raredisease-add-haplocheck-to-qc

How to test

• Do cg workflow raredisease metrics-deliver amusingmarmoset

Expected test outcome

• Check that command completes without errors.

• Check that the new metrics are in the output yaml.
• Take a screenshot and attach or copy/paste the output.

Confirmed the calculated adapter cutoff in excel using PF_BASES as input:

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 great 💯

[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

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