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fix: QC panel bed version generalisation #855

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merged 4 commits into from
Feb 7, 2022
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@ivadym ivadym commented Jan 27, 2022

This PR:

Fixes #854.

Review and tests:

  • Condition (METRIC constant):

Screen Shot 2022-02-04 at 14 47 42

  • Extracted metrics (<case_id>_metrics_deliverables.yaml):

Screen Shot 2022-02-04 at 14 43 30

Screen Shot 2022-02-04 at 14 43 15

  • Validation successfully fails for the panel.bed test file (BALSAMIC.TN_panel.all.0.sh_<job_id>.err):

Screen Shot 2022-02-04 at 14 51 31

@ivadym ivadym linked an issue Jan 27, 2022 that may be closed by this pull request
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codecov bot commented Jan 27, 2022

Codecov Report

Merging #855 (5c2e1b6) into develop (4e29a32) will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff            @@
##           develop     #855   +/-   ##
========================================
  Coverage    99.65%   99.65%           
========================================
  Files           29       29           
  Lines         1759     1759           
========================================
  Hits          1753     1753           
  Misses           6        6           
Flag Coverage Δ
unittests 99.65% <ø> (ø)

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Impacted Files Coverage Δ
BALSAMIC/constants/quality_check_reporting.py 100.00% <ø> (ø)

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sonarqubecloud bot commented Feb 1, 2022

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 marked this pull request as ready for review February 4, 2022 14:00
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ivadym commented Feb 4, 2022

I also added some default conditions for PANEL analysis since some of the bed files validation criteria are not covered in the documentation:

"MEDIAN_TARGET_COVERAGE": {"condition": {"norm": "gt", "threshold": 500}},
"FOLD_80_BASE_PENALTY": {"condition": {"norm": "lt", "threshold": 1.8}},

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👍🏼

@ivadym ivadym merged commit b4cda37 into develop Feb 7, 2022
@ivadym ivadym deleted the fix/QC_panel_bed_version branch February 7, 2022 14:34
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ivadym commented Feb 7, 2022

Updated balsamic.sif container in stage!

@ashwini06 ashwini06 mentioned this pull request Apr 5, 2022
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Successfully merging this pull request may close these issues.

bug: generalise QC validation for different panel versions
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