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chore: add QC criteria for lymphoma_MRD #1479

Merged
merged 8 commits into from
Oct 16, 2024
Merged

chore: add QC criteria for lymphoma_MRD #1479

merged 8 commits into from
Oct 16, 2024

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mathiasbio
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@mathiasbio mathiasbio commented Sep 20, 2024 •
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Description

New lymphoma_mrd panel has been added to production and it needs a QC threshold: #1478

Added

  • QC threshold for lymphoma_MRD panel

Documentation

  • N/A
  • Updated Balsamic documentation to reflect the changes as needed for this PR.
    • [Document Name]

Tests

Feature Tests

  • N/A
  • Test running an example case of the panel and ensure that the QC check is running without errors
  • lymphoma_MRD QC threshold is used:

image

Pipeline Integrity Tests

  • Report deliver (generation of the .hk file)
    • N/A
    • Verified
  • TGA T/O Workflow
    • N/A
    • Verified
  • TGA T/N Workflow
    • N/A
    • Verified
  • UMI T/O Workflow
    • N/A
    • Verified
  • UMI T/N Workflow
    • N/A
    • Verified
  • WGS T/O Workflow
    • N/A
    • Verified
  • WGS T/N Workflow
    • N/A
    • Verified
  • QC Workflow
    • N/A
    • Verified
  • PON Workflow
    • N/A
    • Verified

Clinical Genomics Stockholm

Documentation

Panel of Normal specific criteria

User Changes

  • N/A
  • This PR affects the output files or results.
    • User feedback is considered unnecessary because [Justification].
    • Affected users have been included in the development process and given a chance to provide feedback.

Infrastructure Changes

  • Stored files in Housekeeper
    • N/A
    • Updated: [Link]
  • CG (CLI and delivered/uploaded files)
    • N/A
    • Updated: [Link]
  • Servers (configuration files on Hasta)
    • N/A
    • Updated: [Link]
  • Scout interface
    • N/A
    • Updated: [Link]

Checklist

Important

Ensure that all checkboxes below are ticked before merging.

For Developers

  • PR Description
    • Provided a comprehensive description of the PR.
    • Linked relevant user stories or issues to the PR.
  • Documentation
    • Verified and updated documentation if necessary.
  • Tests
    • Described and tested the functionality addressed in the PR. (NA)
    • Ensured integration of the new code with existing workflows. (NA)
    • Confirmed that meaningful unit tests were added for the changes introduced. (NA)
    • Checked that the PR has successfully passed all relevant code smells and coverage checks.
  • Review
    • Addressed and resolved all the feedback provided during the code review process.
    • Obtained final approval from designated reviewers.

For Reviewers

  • Code
    • Code implements the intended features or fixes the reported issue.
    • Code follows the project's coding standards and style guide.
  • Documentation
    • Pipeline changes are well-documented in the CHANGELOG and relevant documentation.
  • Tests
    • The author provided a description of their manual testing, including consideration of edge cases and boundary
      conditions where applicable, with satisfactory results.
  • Review
    • Confirmed that the developer has addressed all the comments during the code review.

@mathiasbio mathiasbio self-assigned this Sep 20, 2024
@mathiasbio mathiasbio added this to the Release 16 milestone Sep 20, 2024
@mathiasbio mathiasbio linked an issue Sep 20, 2024 that may be closed by this pull request
[Maintenance] Add QC criteria for bait set Lymphoma MRD #1478
Open
3 tasks
@mathiasbio mathiasbio marked this pull request as ready for review September 20, 2024 14:01
@mathiasbio mathiasbio requested a review from a team as a code owner September 20, 2024 14:01
@codecov Codecov
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codecov bot commented Sep 20, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.48%. Comparing base (7d529e6) to head (cc5c713).
Report is 15 commits behind head on develop.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1479   +/-   ##
========================================
  Coverage    99.48%   99.48%           
========================================
  Files           40       40           
  Lines         1932     1957   +25     
========================================
+ Hits          1922     1947   +25     
  Misses          10       10
Flag Coverage Δ
unittests 99.48% <ø> (+<0.01%) ⬆️

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@sonarcloud SonarCloud
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sonarcloud bot commented Oct 15, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

khurrammaqbool
khurrammaqbool approved these changes Oct 15, 2024
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👍

@mathiasbio mathiasbio merged commit 4937d2d into develop Oct 16, 2024
8 checks passed
@mathiasbio mathiasbio deleted the add_lymphoma_mrd_criteria branch October 16, 2024 07:22
@mathiasbio mathiasbio mentioned this pull request Oct 17, 2024
Merged
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Reviewers

@khurrammaqbool khurrammaqbool khurrammaqbool approved these changes

@moahaegglund moahaegglund Awaiting requested review from moahaegglund

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@mathiasbio mathiasbio

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BALSAMIC
Status: Completed
Milestone
Release 16
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Successfully merging this pull request may close these issues.

[Maintenance] Add QC criteria for bait set Lymphoma MRD
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@mathiasbio @khurrammaqbool