fix: Increase vardict tumor only cores allocation to 18

[khurrammaqbool]

Description

During validation, a we noticed that cores allocation for vardict_tumor_only is variable from 5 to 10 for different chromosomes. We did not observe the same problem for tumor-only, which allocates 18 cores, so this PR will increase number of cores from 9 to 18 for vardict_tumor_only.

Fixed

• Increase allocation of cores for vardict_tumor_only to 18

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]

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]

Checklist

Important

Ensure that all checkboxes below are ticked before merging.

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• PR Description
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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.49%. Comparing base (03ddaf0) to head (b407b3e).
Report is 1 commits behind head on release_v16.0.0.

Additional details and impacted files

@@               Coverage Diff                @@
##           release_v16.0.0    #1495   +/-   ##
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  Coverage            99.49%   99.49%           
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  Files                   40       40           
  Lines                 1991     1991           
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  Hits                  1981     1981           
  Misses                  10       10           

Flag	Coverage Δ
unittests	99.49% <ø> (ø)

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[mathiasbio]

Nice! Let's see if this works 🙏

[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 SonarCloud

[mathiasbio]

Tested the new threads on a tumor only case and the provided cores are all 18 now. So assuming that this was the issue, it has been fixed. But let's keep an eye out for it after deployment in case we need to make a fix