feat: automatic download of cytoband coordinates file via init command

[beatrizsavinhas]

Description

Add cytoband coordinates file to list of reference files to automatically download when the init command is run.

Closes #1650.

Added

• The cytoband_coordinates_file to REFERENCE_FILES dict for GenomeVersion.HG19.
  • Specify "dir_name": "genome", file type, name and gzip for the cytoband_coordinates_file.
• The cytoband_coordinates_file to the ReferencesHg model.
• The cytoband_coordinates_file to the list returned by CacheConfig.get_reference_output_paths.
• The cytoband_coordinates_file to the AnalysisReferencesHg model and the object returned by get_analysis_references.
• The cytoband_coordinates_file to pytest.fixture fixture_analysis_references_hg_data.

Changed

• test_get_reference_file_paths_by_compression to include the additional file.
• test_get_reference_output_paths to include the additional file.
• test_get_reference_file_paths_by_compression to include the additional file.

Documentation

• N/A

Tests

Feature Tests

• Install balsamic version from this branch pip install --no-build-isolation --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC@1650-add-cytoband-to-init

• Remove /home/proj/stage/cancer/balsamic_cache/develop/hg19/analysis_finished_successfully file to be able to run init command

• Run init command:

   balsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key COSMIC_KEY --genome-version hg19 --cache-version develop --run-mode local --snakemake-opt "--cores 1" -r

• Check that the cytoBand coordinates file is added to the config.json file:
  

• Check that the cytoBand coordinates file is added to the reference.json file:
  

• Check that cytoBand.txt.gz file exists:
  

Pipeline Integrity Tests

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

Clinical Genomics Stockholm

Documentation

• Atlas documentation
  • N/A
• Web portal for Clinical Genomics
  • N/A

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 does not change output files. Changes for the user will only be implemented in feat: add extra TGA cnv report #1648.

Infrastructure Changes

• Stored files in Housekeeper
  • N/A
• CG (CLI and delivered/uploaded files)
  • N/A
• Servers (configuration files on Hasta)
  • N/A
• Scout interface
  • N/A

Validation criteria

• N/A

Version specific criteria

• 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.
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  • 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 99.38%. Comparing base (7d529e6) to head (5458ec1).
⚠️ Report is 154 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1651      +/-   ##
===========================================
- Coverage    99.48%   99.38%   -0.10%     
===========================================
  Files           40       40              
  Lines         1932     1964      +32     
===========================================
+ Hits          1922     1952      +30     
- Misses          10       12       +2     

Flag	Coverage Δ
unittests	99.38% <100.00%> (-0.10%)	⬇️

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[mathiasbio]

Looks great! 🌟 Thanks a lot! After this is merged I'll update my PR to read from the config instead of directly from the assets/analysis_metadata folder.

Just added a small name change suggestion. But feel free to ignore if you don't agree. If you happen to agree, I don't think you need to test 🙏

[beatrizsavinhas]

Looks great! 🌟 Thanks a lot! After this is merged I'll update my PR to read from the config instead of directly from the assets/analysis_metadata folder.

Just added a small name change suggestion. But feel free to ignore if you don't agree. If you happen to agree, I don't think you need to test 🙏

Thank you!!! 🌟

Totally agree with the name change! Will change it.

[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