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Release browser hail tables #1583

Merged
merged 6 commits into from
Aug 29, 2024
Merged

Release browser hail tables #1583

merged 6 commits into from
Aug 29, 2024

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rileyhgrant
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@rileyhgrant rileyhgrant commented Jun 25, 2024

Resolves #1369

Adds a help page (à la the v4 hail table help page) that describes the gnomAD browser hail tables (variants, gene models).

Reviewing this PR mostly entails taking a glance over the help text to see if there's anything incorrect or misleading.

@rileyhgrant rileyhgrant self-assigned this Jun 25, 2024
@rileyhgrant rileyhgrant marked this pull request as ready for review July 10, 2024 14:00
@rileyhgrant rileyhgrant force-pushed the add-browser-table-helptext branch 2 times, most recently from 36f6674 to 87e6c78 Compare August 5, 2024 19:46
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Files to sync are:

  • gs://gnomad-v4-data-pipeline/output/genes/genes_grch37_annotated_5.ht
  • gs://gnomad-v4-data-pipeline/output/genes/genes_grch38_annotated_5_no_constraint.ht
  • gs://gnomad-v4-data-pipeline/output/gnomad_v4/gnomad_v4_variants_annotated_4.ht

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@nadeaujoshua nadeaujoshua left a comment

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Hey this looks good. I flagged what looks like a few typos.

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@mattsolo1 mattsolo1 requested a review from ch-kr August 7, 2024 14:49
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@ch-kr ch-kr left a comment

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thank you for adding! I've added some minor comments and suggestions, mostly to help clarify the descriptions

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Thanks, all, for the comments. Going to be working through them right now.

Thanks especially to KC for your patience, and for going through this whole blurb of text multiple times now.

@rileyhgrant rileyhgrant force-pushed the add-browser-table-helptext branch 4 times, most recently from ea308ca to 68481d7 Compare August 8, 2024 18:33
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@ch-kr ch-kr left a comment

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a few more minor things -- thanks for your patience with my nitpicks!

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Hiya @ch-kr, this should be ready for your re-review, at your convenience.

Apart from addressing the comments there's a few added things (downloads page with placeholder links, the changelog post , and documenting of the VRS annotations and the joint frequency annotation).

Thank you!!

@rileyhgrant rileyhgrant requested a review from ch-kr August 20, 2024 19:37
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thank you for adding the downloads! a few more minor things, otherwise LGTM. the one thing that needs updating is in data-pipeline/src/data_pipeline/data_types/gene.py (it looks like a bug to me)

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@rileyhgrant rileyhgrant force-pushed the add-browser-table-helptext branch 14 times, most recently from 7ff320c to 26d5734 Compare August 28, 2024 21:03
@rileyhgrant rileyhgrant force-pushed the add-browser-table-helptext branch 3 times, most recently from afd0d3a to 0f1b1a9 Compare August 28, 2024 21:19
@rileyhgrant rileyhgrant merged commit e313c00 into main Aug 29, 2024
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@rileyhgrant rileyhgrant deleted the add-browser-table-helptext branch August 29, 2024 17:32
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Document schema/fields in browser release and gene model HTs
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