chore: clean up

[mathiasbio]

Description

I installed this balsamic env with: conda create --name D_balsamic_log_cleanup -c conda-forge python=3.11 pip "cython<3" pygraphviz wkhtmltopdf snakemake-executor-plugin-slurm=1.7.0

Which means the executor plugin is pinned to 1.7.0 and will work with the slurm_extra qos argument currently in production.

Changed

• moved default resource allocation to snakemake command chore: clean up  #1632
• increased memory of samtools fixmate chore: clean up  #1632
• no rerun for rule all chore: clean up  #1632
• increased head-job runtime to 7 days chore: clean up  #1632
• add attempt mem bump to vep_somatic_research_sv chore: clean up  #1632

Removed

• exome argument panel bed callback function chore: clean up  #1632
• removed -l flag in head-job sbatch script chore: clean up  #1632

Documentation

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

Tests

Feature Tests

• Confirm workflows can finish successfully:
• TGA TO
• TGA exome
• WGS T+N
• Ensure --exome argument order does not matter for config case
• Ensure --exome flag still requires --panel-bed
• Verify that rule all has longer max runtime than 2 minutes: set to 1 hour!
• Verified that memory bump works with attempt in vep_somatic_research_sv

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 (ed8fc37).
⚠️ Report is 142 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1632      +/-   ##
===========================================
- Coverage    99.48%   99.33%   -0.15%     
===========================================
  Files           40       40              
  Lines         1932     1958      +26     
===========================================
+ Hits          1922     1945      +23     
- Misses          10       13       +3     

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

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[fevac]

Looks great thanks! 🌟 If slurm_qos still has issues, let's revert it and continue as is now. Check the comments about fixing resources

[fevac]

Looks great 🌟

[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