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add exome flag to exome samples #3061

Merged
merged 26 commits into from
Apr 10, 2024
Merged

add exome flag to exome samples #3061

merged 26 commits into from
Apr 10, 2024

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mathiasbio
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@mathiasbio mathiasbio commented Mar 21, 2024 •
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DONT MERGE UNTIL RELEASE 15 IN BALSAMIC IS VALIDATED AND DEPLOYED

Description

Adds a new argument for WES applications to add the argument --exome to balsamic config case. This will be necessary to merge for the deployment of balsamic release 15: Clinical-Genomics/BALSAMIC#1422

Added

  • --exome argument to balsamic for samples with wes application tags

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 [THIS-BRANCH-NAME] -a

How to test

  • install balsamic release 15 to stage feat: Release v15.0.0 BALSAMIC#1422
  • run an exome case and verify that the exome tag has been supplied
  • run a non-exome TGA case and verify that exome tag has NOT been supplied

Expected test outcome

In exome case balsamic config json:

image

In TGA non-exome case balsamic config json:
image

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 ...

ivadym
ivadym reviewed Mar 21, 2024
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🔥

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@mathiasbio mathiasbio marked this pull request as ready for review March 25, 2024 07:59
@mathiasbio mathiasbio requested a review from a team as a code owner March 25, 2024 07:59
ivadym
ivadym approved these changes Mar 25, 2024
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Well done 💯

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@mathiasbio mathiasbio self-assigned this Mar 25, 2024
@mathiasbio mathiasbio mentioned this pull request Mar 25, 2024
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henrikstranneheim
henrikstranneheim reviewed Mar 26, 2024
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Great that you are starting to make PRs in cg, 👍 . I have some comments.

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ivadym
ivadym approved these changes Mar 27, 2024
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@mathiasbio
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Thanks a lot for the reviews! ❤️

henrikstranneheim
henrikstranneheim reviewed Mar 27, 2024
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Nice, almost there 😄 !

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@mathiasbio
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Did tests again, and it all still works 👍

ivadym
ivadym reviewed Mar 28, 2024
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💯 🔥

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henrikstranneheim
henrikstranneheim requested changes Apr 3, 2024
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👍

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henrikstranneheim approved these changes Apr 9, 2024
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great! 👍

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed 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

@mathiasbio mathiasbio merged commit 8284ec4 into master Apr 10, 2024
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@mathiasbio mathiasbio deleted the add_apply_balsamic_exome_tag branch April 10, 2024 13:06
@mathiasbio mathiasbio mentioned this pull request Oct 17, 2024
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@ivadym ivadym ivadym approved these changes

@henrikstranneheim henrikstranneheim henrikstranneheim approved these changes

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