[project-defiant]

Summary

The 2026-08-28 GWAS Catalog summary statistics PICS run was moved from the root of gs://gwas_catalog_sumstats_pics into a dated run folder, so the release is preserved before the DAG runs on gentropy v4.0.0 with the new credible set schema. As for the top hits (#220), this allows comparing the results and rolling back.

gs://gwas_catalog_sumstats_pics/prod/20260828T115527/
├── config/gwas_catalog_sumstats_pics.yaml   # DAG config of the run
├── docs/                                    # README.md + DAG svg
└── output/{study_index, study_locus_window_based_clumped, study_locus_ld_clumped, credible_sets}

The timestamp is the time of the first object written by the run (the study index, 2026-08-28T11:55:27Z).

This PR points the repo at the new location:

• gwas_catalog_sumstats_pics.yaml: output_path is now gs://gwas_catalog_sumstats_pics/prod/20260828T115527/output. It is identical to the config uploaded to the run folder; the rest of the config (sync_date: '20260802', GENTROPY_REF: v3.4.0-rc.3) is the one of the run.
• pis/config.yaml: the GCSS PICS study index and credible sets are copied from the run's output/. The data is the same v3 release: pis moves to the v4 outputs once the credible set validation reads CredibleSet and CredibleSetVariant.
• Docs: the sumstats PICS section moves to docs/datasources/gwas_catalog_data/gwas_catalog_sumstats_pics/README.md. The new README:
  • lists the inputs of the run: the gentroutils sync of 2026-08-02, the harmonised summary statistics and the gnomAD LD index
  • describes the four steps, with gentropy links pinned to v3.4.0-rc.3
  • has schema tables of the four outputs, read from the parquet files, with a description per field and the columns with no values marked "Empty"
  • The DAG svg is regenerated and moves next to the README. The GWAS Catalog README links to the new page and gets a changelog entry.
• Makefile: upload-gwas-catalog-sumstats-pics-readme uploads only the sumstats PICS docs to $(BUCKET)/docs, and fails when BUCKET is not set (make upload-gwas-catalog-sumstats-pics-readme BUCKET=gs://gwas_catalog_sumstats_pics/prod/20260828T115527). It is not part of update-bucket-docs. The GWAS Catalog upload no longer copies the full docs to the sumstats PICS bucket.

The bucket is already in this state. The data was copied, and the config and docs were uploaded; the files in this PR are identical to the uploaded copies.

After merge

• Delete the old folders at the root of the bucket, still read by pis on main until this is merged: study_index/, study_locus_window_based_clumped/, study_locus_ld_clumped/, credible_sets/ and docs/.

Notes

• With output_path pinned to the run folder, running the old DAG again would overwrite this release. The next run moves the DAG to StagingDagConfig on gentropy v4 with its own run folder.

Test plan

• uv run pytest tests/test_dag_validation.py (orchestration): 10 passed
• uv run pytest tests (pis): 10 passed
• make -n upload-gwas-catalog-sumstats-pics-readme fails without BUCKET and resolves to the run folder with it
• README, svg and config in the PR are byte-identical to gs://gwas_catalog_sumstats_pics/prod/20260828T115527/
• the copied outputs match the root folders: same bytes and the same crc32c of every object
• study_index/*.parquet (1 file) and credible_sets/*.parquet (23 files) globs in pis/config.yaml match files in the run folder

🤖 Generated with Claude Code

[addramir]

Looks good. Merges clean on current main and matches the #220 pattern.

• upload-gwas-catalog-sumstats-pics-readme (and the top hits one) is missing from .PHONY.
• upload-gwas-catalog-buckets-readme still copies the new gwas_catalog_sumstats_pics/ subfolder to gs://gwas_catalog_inputs/docs and gs://gwas_catalog_sumstats_susie/docs. Fine for now; worth a follow-up.
• ../README.md#gwas-catalog-inputs will not resolve in the copy under $(BUCKET)/docs.