feat: update sentieon to version 202308.02

[mathiasbio]

Description

This PR does not aim to include many updates in terms of analysis, but mainly serve to verify the continued integrity and performance of the workflows after updating the Sentieon version, as well as update the docs.

However, making the update might require some changes to the workflow. But these will be kept to a minimum.

NOTE: The actual update will be done in the servers repository: https://github.com/Clinical-Genomics/servers/blob/master/resources/hasta.scilifelab.se/start_sentieon_function.sh

Added

• [Description]

Changed

• [Description]

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]

Workflow quality verifications (half-mimicking validation)

See google sheet for detailed results: https://docs.google.com/spreadsheets/d/1hSX1xGqsHwWZAgfITwKZTNVYZCVITHtN3fK2t-_S1g8/edit#gid=0

Test status:

• [ ] PASS

Pipeline Integrity Tests

• Report deliver (generation of the .hk file)
  • [x] N/A
  • [ ] Verified
• TGA T/O Workflow
  • [x] N/A
  • [ ] Verified
• TGA T/N Workflow
  • [x] N/A
  • [ ] Verified
• UMI T/O Workflow
  • [x] N/A
  • [ ] Verified
• UMI T/N Workflow
  • [x] N/A
  • [ ] Verified
• WGS T/O Workflow
  • [x] N/A
  • [ ] Verified
• WGS T/N Workflow
  • [x] N/A
  • [ ] Verified
• QC Workflow
  • [x] N/A
  • [ ] Verified
• PON Workflow
  • [x] N/A
  • [ ] Verified

Clinical Genomics Stockholm

Documentation

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

User Changes

• [x] 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
  • [x] N/A
  • [ ] Updated: [Link]
• CG (CLI and delivered/uploaded files)
  • [x] N/A
  • [ ] Updated: [Link]
• Servers (configuration files on Hasta)
  • [x] N/A
  • [ ] Updated: [Link]
• Scout interface
  • [x] 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.