feat: Update TIDDIT version to 3.9.3

[kristinebilgrav]

Description

Closes #1467

[PR description]

Added

• [Description]

Changed

• Updated tiddit from 3.3.2 to 3.9.3

Fixed

• [Description]

Removed

• [Description]

Documentation

• N/A
• Updated Balsamic documentation to reflect the changes as needed for this PR.
  • Readthedocs

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]

Validation criteria

Validation criteria to be added to validation report PR: [LINK-TO-VALIDATION-REPORT-PR from the validations repository]

Version specific criteria

• Text here or N/A

Important

One of the below checkboxes for validation need to be checked

• Added version specific validation criteria to validation report
• Changes validated in standard sections: [validation-section]
• Validation criteria not necessary

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.
• Validation criteria
  • Completed the validation criteria section of the template.
• 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.
• Validation criteria
  • The author has completed the validation criteria section of the template
• 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 99.33%. Comparing base (7d529e6) to head (18d8e15).
⚠️ Report is 152 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1647      +/-   ##
===========================================
- Coverage    99.48%   99.33%   -0.15%     
===========================================
  Files           40       40              
  Lines         1932     1959      +27     
===========================================
+ Hits          1922     1946      +24     
- Misses          10       13       +3     

Flag	Coverage Δ
unittests	99.33% <100.00%> (-0.15%)	⬇️

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[mathiasbio]

Looks great! 🌟 🌟

It would be nice to see in general if the pipeline still finishes successfully now given these changes, and I think that as the varcall_py3 container has also been updated it might make sense to run a TGA T+N case as well, just to ensure that everything is still working.

For the TIDDIT update itself, it would also be nice to have a small comparison of the case run with the old and new version of TIDDIT, just to understand how the number of variants are affected, and if there's any new filter or something that we might need to take into account 🤔

If any of the cases here were used in the testing it could also be a small sanity check to see if the variant listed there is still detected by TIDDIT: https://github.com/Clinical-Genomics/validations/blob/main/docs/pipelines/balsamic/balsamic18.0_validation_report.md#wgs-cases-with-confirmed-svs-extended

[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 SonarQube Cloud