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fix: CNVkit container #1457
fix: CNVkit container #1457
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1457 +/- ##
========================================
Coverage 99.48% 99.48%
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Files 40 40
Lines 1932 1944 +12
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+ Hits 1922 1934 +12
Misses 10 10
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
Quality Gate passedIssues Measures |
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Sweet! Nicely done! :D 🌟
Description
Fix and clean CNVkit container.
Originally, I intended to update CNVkit to version 0.9.11. However, the new release includes some lazy requirements to fix previous dependency issues, which now block and break the installation. This has been reported in their issues. Therefore, I'm sticking with the previous version and pinning numpy to ensure the tools don't break.
Fixed
Documentation
Tests
Feature Tests
cnvkit_segment_CNV_research
does not break due to numpy major version release:Pipeline Integrity Tests
.hk
file)Clinical Genomics Stockholm
Documentation
Panel of Normal specific criteria
User Changes
Infrastructure Changes
Checklist
Important
Ensure that all checkboxes below are ticked before merging.
For Developers
For Reviewers
conditions where applicable, with satisfactory results.