feat: add extra TGA cnv report

[mathiasbio]

Description

Closes: #1554

Added

• add new CNV html report
• add cust-case-id to case config and CNV plots
• add cancer-genelist with cancer genes from custs and oncokb
• add bcftools split multialleles for DNAscope calls
• add germline vcf to create VAF plot in CNVkit scatter

Changed

• changed DNAscope germline panel bedfile to padded bed
• renamed old CNV pdf report for TGA to signify it is deprecated

Fixed

• [Description]

Removed

• removed unused CNV report snakemake rule

Documentation

• N/A
• Updated Balsamic documentation to reflect the changes as needed for this PR.
  • Add documentation PR: docs: add CNV report docs #1665

Tests

Feature Tests

Example CNV reports on CG drive

• CNV report can be created without optional files
• without PureCN LOH regions file
• without PON file
• new CNV report can be stored in housekeeper with hermes PR: Balsamic 19 changes hermes#161
• old CNV deprecated report can be stored in housekeeper with hermes PR, with scout tag removed: Balsamic 19 changes hermes#161
• WGS case still produce CNV report in the list of files to deliver
• new CNV report is automatically uploaded to Scout (cg upload -c fails due to GENS issue, testing with cg upload create-scout-load-config CASE ; cg upload upload-case-to-scout CASE -r) See link in this PR: Balsamic 19 changes hermes#161

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.

[fevac]

@mathiasbio don't forget to update the description of the PR

[fevac]

Pending documentation to be added in a different PR and pytests

[mathiasbio]

Thanks so much again for all the reviews @fevac ! I have added the documentation and the pytests now.

Regarding the renaming I decided to go with the change to "report.pdf" --> "report_deprecated.pdf" however as this also would have impacted the WGS workflow I needed to make a minor change there to make WGS still produce the original file name for the report.

I'm just testing now that it is still working for both analysis types

[fevac]

Regarding the renaming I decided to go with the change to "report.pdf" --> "report_deprecated.pdf" however as this also would have impacted the WGS workflow I needed to make a minor change there to make WGS still produce the original file name for the report.

Hi @mathiasbio I don't like this approach. When we talked we didn't consider that the WGS pdf report will still be used and not deprecated. Given that WGS cnv reports will continue to be generated, I would rather rename the html report and leave the original pdf report as-is. I'll update the code and hermes

[fevac]

setamoeba failing with:

    raise TemplateNotFound(template)
jinja2.exceptions.TemplateNotFound: cnv_report.html.j2

fixed by adding extensions to setup file

[sonarqubecloud]

Quality Gate passed

Issues
23 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
2.9% Duplication on New Code

See analysis details on SonarQube Cloud