feat: Release v17.1.0

[mathiasbio]

Description

Minor release update to fix this issue which has unfortunately caused significant problems in production: #1345

Deviation: https://github.com/Clinical-Genomics/Deviations/issues/812

PRs to be merged into this:

• feat: remove ref strand filter from WGS TO: feat: remove ref strand filter from WGS TO #1594

VERIFICATION REPORT ISSUE: #1595

Changed

• changed strand bias filter for WGS TO SNV quality filter to only require representation from both strands in alt allele
• lowered maximum raredisease loqusdb SNV observation frequency from 0.01 to 0.007, and verified no common cancer predisposition variant exists above that threshold

Documentation

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

Tests

Feature Tests

• N/A
• Tested in PRs and verification report

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: Validated here: Verification Report [v17.1.0] #1595
• 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.

[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

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.40%. Comparing base (1b49253) to head (5974fb2).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1593   +/-   ##
=======================================
  Coverage   99.40%   99.40%           
=======================================
  Files          40       40           
  Lines        2019     2019           
=======================================
  Hits         2007     2007           
  Misses         12       12           

Flag	Coverage Δ
unittests	99.40% <ø> (ø)

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[rannick]

LGTM!