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🚧 exome/panel genotyping #53

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🚧 exome/panel genotyping #53

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Description

Reworking our single sample genotyping workflow to be able to handle Exome and Targeted Sequencing input samples.

Part of https://d3b.atlassian.net/browse/BIXU-3800

Type of change

  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

Test Configuration:

  • Environment:
  • Test files:

Checklist:

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes
  • Any dependent changes have been merged and published in downstream modules
  • I have checked my code and corrected any misspellings
  • I have committed any related changes to the PR

@dmiller15 dmiller15 added feature New functionality bix-dev This issue or pull request is bix-dev work labels Dec 19, 2024
@dmiller15 dmiller15 self-assigned this Dec 19, 2024
migbro
migbro approved these changes Dec 19, 2024
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@migbro migbro left a comment

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A great start overall. Nice to have a lot of this modernized and cleaned up

tools/gatk_applyrecalibration.cwl Show resolved Hide resolved
tools/gatk_genomicsdbimport_genotypegvcfs.cwl Show resolved Hide resolved
tools/gatk_indelsvariantrecalibrator.cwl Show resolved Hide resolved
workflows/kfdrc-single-sample-genotyping-wf.cwl Show resolved Hide resolved
tools/filtering_defaults.cwl Show resolved Hide resolved
@dmiller15 dmiller15 force-pushed the dm-exome-panel-genotyping branch from 29c3956 to 4ee1df2 Compare December 19, 2024 16:51
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@migbro migbro migbro approved these changes

@sickler-alex sickler-alex Awaiting requested review from sickler-alex

@wongjessica93 wongjessica93 Awaiting requested review from wongjessica93

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@dmiller15 @migbro