fix: update MSI table

[khurrammaqbool]

Description

Update MSI final table.

Added

• [Description]

Changed

• MSI final table

Fixed

• [Description]

Removed

• [Description]

Documentation

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

Tests

Feature Tests

• N/A
• Test [Description]
  • [Screenshot]

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

• Atlas documentation
  • N/A
  • Updated: [Link]
• Web portal for Clinical Genomics
  • N/A
  • Updated: [Link]

Panel of Normal specific criteria

• The PR includes the addition of a new Panel of Normals
• The samples have been verified to adhere to the sample selection criteria on Atlas PoN creation instructions for Balsamic

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
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  • Confirmed that meaningful unit tests were added for the changes introduced.
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• Code
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  • Pipeline changes are well-documented in the CHANGELOG and relevant documentation.
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[khurrammaqbool]

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.48%. Comparing base (7d529e6) to head (3cec71e).
Report is 10 commits behind head on develop.

❗ Current head 3cec71e differs from pull request most recent head 19bfe34

Please upload reports for the commit 19bfe34 to get more accurate results.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1459   +/-   ##
========================================
  Coverage    99.48%   99.48%           
========================================
  Files           40       40           
  Lines         1932     1944   +12     
========================================
+ Hits          1922     1934   +12     
  Misses          10       10           

Flag	Coverage Δ
unittests	99.48% <ø> (+<0.01%)	⬆️

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[mathiasbio]

Nice! Do you think we need to high some explanation for what the scores mean, or is it up to the clinicians to understand how to use the score?

[khurrammaqbool]

Nice! Do you think we need to high some explanation for what the scores mean, or is it up to the clinicians to understand how to use the score?

The references from the article would be nice to know more about what the score mean. Perhaps, these two review articles may be a good starting point: https://doi.org/10.3389/fonc.2018.00621 and https://doi.org/10.1093/gbe/evq023.
This request to add MSI came from the customer so I am sure they know what the score mean.

[mathiasbio]

Alright! 👍

[mathiasbio]

Looks good to me! 🌟

[ivadym]

👍

Please use the template Test section in your next PRs with a description of what has been tested, instead of posting the results in separate messages. Thanks!

[sonarqubecloud]

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