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Add Balsamic validated metrics to delivery report #2688

Merged
merged 14 commits into from
Nov 21, 2023
Merged

Add Balsamic validated metrics to delivery report #2688

merged 14 commits into from
Nov 21, 2023

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ivadym
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@ivadym ivadym commented Nov 14, 2023 •
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Description

Added

  • Missing Balsamic metrics used for Balamic QC validation

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

  • cg generate delivery-report <case-id> (TGA)
  • cg generate delivery-report <case-id> (WGS)

Expected test outcome

  • GC dropout in delivery report for TGA
Screenshot 2023-11-20 at 18 15 25
  • Reads with improper pairs for WGS
Screenshot 2023-11-20 at 18 13 31

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 changed the title Add Balsamic QC validated metrics to delivery report Add Balsamic validated metrics to delivery report Nov 14, 2023
@ivadym ivadym self-assigned this Nov 14, 2023
@ivadym ivadym marked this pull request as ready for review November 20, 2023 13:02
@ivadym ivadym requested a review from a team as a code owner November 20, 2023 13:02
@ivadym ivadym requested a review from karlnyr November 20, 2023 13:02
karlnyr
karlnyr approved these changes Nov 20, 2023
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Neat!

cg/meta/report/templates/balsamic_report.html Outdated Show resolved Hide resolved
cg/meta/report/templates/balsamic_report.html Outdated Show resolved Hide resolved
diitaz93
diitaz93 approved these changes Nov 20, 2023
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Looks good 👍

cg/constants/report.py Outdated Show resolved Hide resolved
@sonarqubecloud SonarQubeCloud
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@ivadym ivadym merged commit 2825552 into master Nov 21, 2023
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@ivadym ivadym deleted the add-metrics-report branch November 21, 2023 08:43
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ivadym commented Nov 21, 2023

Screenshot 2023-11-21 at 10 16 57

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@karlnyr karlnyr karlnyr approved these changes

@diitaz93 diitaz93 diitaz93 approved these changes

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@ivadym @diitaz93 @karlnyr