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feat(staging):updates for staging data release 2025.03 #102

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merged 7 commits into from
Feb 5, 2025

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@project-defiant project-defiant commented Feb 5, 2025

Context

This PR closes https://github.com/orgs/opentargets/projects/31?pane=issue&itemId=91225382&issue=opentargets%7Cissues%7C3699

This PR sums changes introduced to run the staging bucket genetics data freeze for:

  • GWAS Catalog
  • UKB PPP
  • Finngen r12
  • eQTL Catalogue

Changes

  • Addition of labels to the fine-mapping google batch job to allow for cost track.
created_by: gentropy-pipelines
environment: development
gentropy_dag: ukb-ppp-eur-susie-finemapping
subteam : genetics
team : open-targets
  • Introduction of date versionning to the staging bucket datasets that undergo finemapping - this allows us to keep track on the changes in between the release
  • Successfull rerun following dags:
    • gwas_catalog_sumstats_susie_clumping
    • gwas_catalog_sumstats_susie_finemapping
    • gwas_catalog_sumstats_pics
    • gwas_catalog_top_hits
    • ukb_ppp_eur_finemapping
    • eqtl_catalogue_ingestion
    • credible_set_qc
  • Change staging bucket configs to use environment variables to define TEST or PROD run mode. (in progress)

@project-defiant project-defiant requested review from Daniel-Considine and removed request for DSuveges February 5, 2025 15:06
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@Daniel-Considine good spot, thanks!

@project-defiant project-defiant merged commit 2572e53 into dev Feb 5, 2025
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3 participants