Run panel PANELAPP-GREEN by default in all MIP runs

[beatrizsavinhas]

Description

Add panel PANELAPP-GREEN to all MIP runs.
Related to issue #2698

Added

• PANELAPP-GREEN to run by default

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-PANELAPP-GREEN-to-mip -a

How to test

• Attempt to run a case with a panel not in master list with cg and note the new panel being fetched from Scout, e.g.

   cg set case justhusky -g OPHTHALMO
   cg workflow mip-dna start justhusky -d

Expected test outcome

• Check that the new panel is being fetched from Scout when running a case with a panel not in master list
• Take a screenshot and attach or 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

• Document in ...
• Deploy this branch on ...
• Inform to ...

[beatrizsavinhas]

@dnil Is this the correct way to do this? Could you help me with testing also? 🤔

[beatrizsavinhas]

Testing

With master:

20d [hiseq.clinical@hasta:~] [S_base] 48s $ cg workflow mip-dna start justhusky -d
(...)
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 OPHTHALMO OMIM-AUTO --build 37

Only OPHTHALMO and OMIM-AUTO loaded.

After deploying this branch:

20d [hiseq.clinical@hasta:~] [S_base] 50s $ cg workflow mip-dna start justhusky -d
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 OPHTHALMO PANELAPP-GREEN OMIM-AUTO --build 37

Panels OPHTHALMO, PANELAPP-GREEN and OMIM-AUTOloaded.

Panel PANELAPP-GREEN loaded successfully!

[diitaz93]

👍

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[beatrizsavinhas]

Deployed to production by BSV:

20d [hiseq.clinical@hasta:~] [base] 3m43s $ bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_cg -t cg -b master -a
(..)
done.
Log deploy... done.
cg, version 53.5.3