fix: tnscope found in

[mathiasbio]

Description

Added TNscope found in to info field and removed VarDict germline filter (which should be replaced by the new relative normal af / tumor af filter)

Added

• [Description]

Changed

• [Description]

Fixed

• TNscope tag to variant info-field for TGA workflow

Removed

• Removed VarDict germline filter, replaced by relative normal af / tumor af filter

Documentation

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

Tests

Feature Tests

• Verify that TNscope and VarDict exists in uploaded twist pancancer reference sample bosscat to Scout:

• Test that variants with "germline" status in VarDict results exists after bcftools quality filters

From selectbengal twist pancancer reference sample:

4 119848931 . T TGATAGATAGATA 194 PASS AF=0.2073;DP=82;LSEQ=TAGATATATAGATAGATAGA;MSI=11;MSILEN=4;RSEQ=GATAGATAGATAGATAGATA;SAMPLE=selectbengal;SHIFT3=32;SOR=3.97429;SSF=0.01912;STATUS=Germline;TYPE=Insertion;VD=17 GT:AD:ADJAF:AF:ALD:BIAS:DP:HIAF:MQ:NM:ODDRATIO:PMEAN:PSTD:QSTD:QUAL:RD:SBF:SN:VD 0/1:14,17:0.0366:0.2073:11,6:2,2:82:1:57:1:1.02:48.6:1:1:47.7:9,5:1:34:17 0/1:4,3:0:0.0612:1,2:2,2:49:0.2:60:1.1:4.4496:39.3:1:1:57:3,1:0.48571:6:3

AF T: 0.2073, AF N: 0.0612

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
  • Verified and updated documentation if necessary.
• Tests
  • Described and tested the functionality addressed in the PR.
  • Ensured integration of the new code with existing workflows.
  • Confirmed that meaningful unit tests were added for the changes introduced.
  • 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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.49%. Comparing base (7fc67a6) to head (57362cd).
Report is 1 commits behind head on release_v16.0.0.

Additional details and impacted files

@@               Coverage Diff                @@
##           release_v16.0.0    #1497   +/-   ##
================================================
  Coverage            99.49%   99.49%           
================================================
  Files                   40       40           
  Lines                 1991     1991           
================================================
  Hits                  1981     1981           
  Misses                  10       10           

Flag	Coverage Δ
unittests	99.49% <ø> (ø)

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[khurrammaqbool]

Please add the screenshot to show found in for TNscope, possibly from Scout as well if this is the intention of the fix.

[sonarcloud]

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