Add panel Inherited cancer to the clinical masterlist

[beatrizsavinhas]

Description

Added

• Panel Inherited cancer to clinical master list

How to prepare for test

• Ssh to hasta
• 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-Inherited-cancer-to-masterlist -a

How to test

• Check if panel is fetched when running a case containing a panel from the masterlist

Expected test outcome

• Check that Inherited cancer appears in the output when running case justhusky
• Copy/paste the output.

Review

• Tests executed by BSV
• "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

• Deploy this branch
• Inform to customer that the change has been deployed

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[beatrizsavinhas]

Testing

20d [hiseq.clinical@hasta:~] [S_base] 130 $ cg workflow mip-dna start justhusky --dry-run
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Case justhusky exists in Status DB
Starting full MIP analysis workflow for case justhusky
Flow cell check is not applicable - the case is either down sampled or external.
Found file earlycasualcaiman/2019-05-08/HHT5NDSXX_HapMap_S26_L001_R1_001.fastq.gz
Found file earlycasualcaiman/2019-05-08/HHT5NDSXX_HapMap_S26_L001_R2_001.fastq.gz
Found file slowlycivilbuck/2019-05-08/HHT5NDSXX_HapMap_S27_L001_R1_001.fastq.gz
Found file slowlycivilbuck/2019-05-08/HHT5NDSXX_HapMap_S27_L001_R2_001.fastq.gz
Found file hugelymodelbat/2019-05-08/HHT5NDSXX_HapMap_S28_L001_R1_001.fastq.gz
Found file hugelymodelbat/2019-05-08/HHT5NDSXX_HapMap_S28_L001_R2_001.fastq.gz
Case justhusky exists in Status DB
Case justhusky exists in Status DB
Running command /home/proj/stage/bin/miniconda3/envs/S_scout/bin/scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml export panel --bed BRAIN Cardiology CILM CH CTD DIAB ENDO EP HEARING HYDRO IBMFS IEM IF mcarta MHT MIT MOVE mtDNA NBS-M NEURODEG NMD OMIM-AUTO PANELAPP-GREEN PEDHEP PID PIDCAD RETINA SKD SOVM STROKE AID Inherited cancer --build 37

Inherited cancer loaded!

[northwestwitch]

Looks good! 💯

[seallard]

👍

[beatrizsavinhas]

Log deploy... done.
cg, version 54.3.0

Deployed successfully.