feat: add Sentieon path argument to config

[mathiasbio]

Description

Adds an argument to balsamic case config which allows for overriding the SENTIEON_INSTALL_DIR in the environment to a chosen path. This would allow us to easier test new versions of Sentieon without needing to make changes in the servers repository, or manually override the environment variables by adding hardcoded paths in the balsamic.smk of the dev-branches.

Together with associated changes in CG we can also start using this argument in production by adding the Sentieon install path to the cg.yaml and supplying it via CG to the case config.

Added

• Sentieon install directory path and Sentieon license to case config arguments

Documentation

• N/A
• Updated Balsamic documentation to reflect the changes as needed for this PR.
  • updated install.rst with new Sentieon argument info

Tests

Feature Tests

• N/A
• Test that using --sentieon-install-dir and --sentieon-license argument puts these variables in config.json and is working
  • In config.json:

• In alignment rule using the supplied version of Sentieon:

• Verify that supplying wrong Sentieon license makes the Sentieon rules fail with invalid license

Pipeline Integrity Tests

Justification for limited pipeline integrity test:

• 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 99.48%. Comparing base (7d529e6) to head (496345b).
Report is 12 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1461   +/-   ##
========================================
  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% <100.00%> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[ivadym]

Looks good overall 💯

I think the review comments may be a bit disorganised, but the main point is to decide if we want to keep the support for the environment variables for the Sentieon license. I don't see any advantages in maintaining that code over time, so I would just stick with the values provided by the CLI

[ivadym]

Nice! Such a clean implementation! 🥇 💯

[ivadym]

Tested with the respective CG branch Clinical-Genomics/cg#3388:

[sonarqubecloud]

Quality Gate failed

Failed conditions
4.6% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud