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Update paths to variant cooccurrence tsv files #1350

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merged 2 commits into from
Dec 6, 2023

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rileyhgrant
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@rileyhgrant rileyhgrant commented Dec 6, 2023

Resolves #1328

  • Minorly updates v2 downloads to use the correct download links
  • Updates the variant coocurrence pipeline task to refer to the publicly released .tsv files
    • Changes the name of a field in the pipeline task to accomodate the field name change in the public file

I tested running the task locally and it succeeds using the public data. I did not run it in the context of the whole pipeline, fwiw, but the return schema from the tasks are unchanged.

@rileyhgrant rileyhgrant force-pushed the update-variant-coocurrence-paths branch from f937fbf to 83588f5 Compare December 6, 2023 20:27
@rileyhgrant rileyhgrant self-assigned this Dec 6, 2023
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Requesting your review on this @phildarnowsky-broad as you've been much closer to this feature and pipeline task.

Very minor update of the task itself to reference the publicly released files, and to transmute the changed field name into the one used throughout the rest of the stack (af_threshold in the input file, rather than af_cutoff)

@rileyhgrant rileyhgrant force-pushed the update-variant-coocurrence-paths branch from db4522a to 4c2af8d Compare December 6, 2023 20:38
@rileyhgrant rileyhgrant merged commit f0aeb2a into main Dec 6, 2023
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@rileyhgrant rileyhgrant deleted the update-variant-coocurrence-paths branch December 6, 2023 20:47
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Access to variant_cooccurrence_counts.py input files
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