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🎉 add hardfilter annotation filter plotting #59

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merged 8 commits into from
Jan 16, 2025

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dmiller15
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@dmiller15 dmiller15 commented Jan 8, 2025

Description

Adds subworkflow to hardfiltering to generate plots for the annotations that are part of the harfiltering process.

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

Type of change

  • New feature (non-breaking change which adds functionality)

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 self-assigned this Jan 8, 2025
@dmiller15 dmiller15 added feature New functionality bix-dev This issue or pull request is bix-dev work labels Jan 8, 2025
@dmiller15 dmiller15 marked this pull request as ready for review January 13, 2025 15:06
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@migbro migbro left a comment

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Unless I am missing something, I think there are a couple minor copy/paste instances that missed some crucial editing in the plot genotyping sub workflow

docs/GERMLINE_SNV_README.md Outdated Show resolved Hide resolved
scripts/gatk_plot_annotations.R Outdated Show resolved Hide resolved
scripts/gatk_plot_annotations.R Show resolved Hide resolved
subworkflows/gatk_plot_genotyping_annotations.cwl Outdated Show resolved Hide resolved
subworkflows/gatk_plot_genotyping_annotations.cwl Outdated Show resolved Hide resolved
@dmiller15 dmiller15 requested a review from migbro January 16, 2025 18:21
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Looks good now, thanks!

@dmiller15 dmiller15 merged commit be19575 into master Jan 16, 2025
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@dmiller15 dmiller15 deleted the dm-plot-hardfilters branch January 16, 2025 18:40
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3 participants