feat: extend bedfiles for CNV analysis

[mathiasbio]

Description

During the work introducing GENS for TGA it was discovered that about half of all regions in the bedfile for GMCKsolid 4.1 was discarded by CNVkit during analysis. This was due to small regions in the bedfile, see issue: #1468

To fix this it was initially planned to update the bedfiles in the target capture repo: https://github.com/Clinical-Genomics/target_capture_bed/issues/133 however there was no easy solution to implement this alternate versions of the bedfiles, and in the end the best way to solve the issue seems to be to extend these short regions dynamically during runtime specifically for the CNV analysis.

This also has the benefit of leaving the SNV and InDel calling, and the QC metrics unchanged.

To achieve this a new rule was added with a extend bed-regions step, followed by bedtools sort and merge to merge potentially overlapping bed regions after the extension.

Added

• padding of bed-regions for CNVkit to minimum 100 bases

Changed

• [Description]

Fixed

• [Description]

Removed

• [Description]

Documentation

• N/A
• Updated Balsamic documentation to reflect the changes as needed for this PR.
  • balsamic_pon.rst updated with minimum region size information

Tests

Feature Tests

• N/A
• Test [Description]
  • [Screenshot]

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: https://github.com/Clinical-Genomics/atlas/pull/2855
• 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: the communication with customers is ongoing for the CNVkit to GENS PR: feat: add tga cnvkit to gens #1448 .
  • 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 ✅

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Additional details and impacted files

@@                  Coverage Diff                  @@
##             update_cnvkit_pons    #1469   +/-   ##
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  Coverage                      ?   99.48%           
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  Files                         ?       40           
  Lines                         ?     1960           
  Branches                      ?        0           
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  Hits                          ?     1950           
  Misses                        ?       10           
  Partials                      ?        0           

Flag	Coverage Δ
unittests	99.48% <100.00%> (?)

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[mathiasbio]

As a note! I wonder if we could skip the workflow integrity checks in this PR since it is a nested PR which I plan to test more thoroughly in the add CNVkit to GENS PR #1448 since that is where I have access to a better way of interpreting the results. So I was thinking I could run all of my tests there. Additionally all PRs will eventually end up in the #1358 PR which I will run some final tests on when everything has been merged. So we're pretty far from the develop branch

[sonarcloud]

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 SonarCloud