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Add plof column anno df #90

Merged
merged 16 commits into from
May 16, 2024
Merged

Add plof column anno df #90

merged 16 commits into from
May 16, 2024

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Marcel-Mueck
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@Marcel-Mueck Marcel-Mueck commented May 16, 2024 •
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What

This PR adds a column is_plof to the annotations, the column is generated from some of the Consequence columns in the annotation pipeline

Testing

  • the compute_ploffunction is tested automatically via github actions
  • the updated pipeline was run locally

Test scenarios

  • running the compute_plof function with two different data sets
  • running the select_rename_fill function including the plof column

endast and others added 15 commits May 16, 2024 10:39
@endast
Add --chromosomes flag to add_variants_id
32ed396
fixup! Format Python code with psf/black pull_request
8e897d3
@endast
Revert "Change actions to us ubuntu-latest"
3d5319d 
This reverts commit 2f821a8.
@endast
Add logging
5c4c5d1
added compute_plof function, added it to pipeline, created tests
3b99da1
plof cast to int values, tests reflect expected change
bf48734
added plof column to annotation_colnames_filling_values.yaml file, ad…
159338d 
…ded test for select_rename_fill function with input containing plof column
reset snakefile to main version
6bb905b
fixup! Format Python code with psf/black pull_request
31e921f
@Marcel-Mueck
Update github-actions.yml
e4963f5
@Marcel-Mueck
Update autoblack_pull_request.yml
9f67f11
@Marcel-Mueck
Update docs-tests.yml
c0c2d50
@Marcel-Mueck
Update test-runner.yml
605b0b7
@Marcel-Mueck
Update .readthedocs.yaml
fc7dc42
added plof rule to snakefile, updated rulegraph in docs
e03876d
@Marcel-Mueck Marcel-Mueck requested a review from endast May 16, 2024 13:19
@Marcel-Mueck Marcel-Mueck added the enhancement New feature or request label May 16, 2024
@Marcel-Mueck Marcel-Mueck marked this pull request as ready for review May 16, 2024 13:19
endast
endast approved these changes May 16, 2024
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Seems to work!

@Marcel-Mueck Marcel-Mueck merged commit 92ea94d into main May 16, 2024
13 checks passed
@Marcel-Mueck Marcel-Mueck deleted the add_plof_column_anno_df branch May 16, 2024 14:24
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@endast endast endast approved these changes

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@Marcel-Mueck @endast