chore: merge main

Author: d0choa

.github/workflows/docs.yaml

@@ -11,7 +11,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.10.8
       - name: Install and configure Poetry

.github/workflows/pytest.yaml

@@ -8,7 +8,7 @@ jobs:
         with:
           fetch-depth: 1
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.10.8
       - name: Install and configure Poetry

config/datasets/gcp.yaml

@@ -32,23 +32,18 @@ variant_annotation: ${datasets.outputs}/variant_annotation
 variant_index: ${datasets.outputs}/variant_index
 study_locus: ${datasets.outputs}/study_locus
 credible_set: ${datasets.outputs}/credible_set
+study_index: ${datasets.outputs}/study_index
+summary_statistics: ${datasets.outputs}/summary_statistics
 study_locus_overlap: ${datasets.outputs}/study_locus_overlap
 colocalisation: ${datasets.outputs}/colocalisation
 v2g: ${datasets.outputs}/v2g
 ld_index: ${datasets.outputs}/ld_index
-catalog_study_index: ${datasets.outputs}/catalog_study_index
-catalog_study_locus: ${datasets.study_locus}/catalog_study_locus
-finngen_study_index: ${datasets.outputs}/finngen_study_index
-finngen_summary_stats: ${datasets.outputs}/finngen_summary_stats
+catalog_study_index: ${datasets.study_index}/catalog_curated
+catalog_study_locus: ${datasets.credible_set}/catalog_curated
+finngen_study_index: ${datasets.study_index}/finngen
+finngen_summary_stats: ${datasets.summary_statistics}/finngen
 from_sumstats_study_locus: ${datasets.study_locus}/from_sumstats
 from_sumstats_pics: ${datasets.credible_set}/from_sumstats
-ukbiobank_study_index: ${datasets.outputs}/ukbiobank_study_index
+ukbiobank_study_index: ${datasets.study_index}/ukbiobank
 l2g_model: ${datasets.outputs}/l2g_model
 l2g_predictions: ${datasets.outputs}/l2g_predictions
-eqtl_catalogue_study_index_out: ${datasets.outputs}/preprocess/eqtl_catalogue/study_index
-eqtl_catalogue_summary_stats_out: ${datasets.outputs}/preprocess/eqtl_catalogue/summary_stats
-
-# Constants
-finngen_release_prefix: FINNGEN_R9
-finngen_sumstat_url_prefix: gs://finngen-public-data-r9/summary_stats/finngen_R9_
-finngen_sumstat_url_suffix: .gz

config/step/finngen.yaml

@@ -1,7 +1,3 @@
 _target_: otg.finngen.FinnGenStep
-finngen_phenotype_table_url: ${datasets.finngen_phenotype_table_url}
-finngen_release_prefix: ${datasets.finngen_release_prefix}
-finngen_sumstat_url_prefix: ${datasets.finngen_sumstat_url_prefix}
-finngen_sumstat_url_suffix: ${datasets.finngen_sumstat_url_suffix}
 finngen_study_index_out: ${datasets.finngen_study_index}
 finngen_summary_stats_out: ${datasets.finngen_summary_stats}

config/step/gwas_catalog.yaml renamed to config/step/gwas_catalog_ingestion.yaml

@@ -4,6 +4,5 @@ catalog_ancestry_files: ${datasets.catalog_ancestries}
 catalog_associations_file: ${datasets.catalog_associations}
 catalog_sumstats_lut: ${datasets.catalog_sumstats_lut}
 variant_annotation_path: ${datasets.variant_annotation}
-ld_index_path: ${datasets.ld_index}
 catalog_studies_out: ${datasets.catalog_study_index}
 catalog_associations_out: ${datasets.catalog_study_locus}

docs/python_api/datasource/gwas_catalog/associations.md

@@ -2,4 +2,8 @@
 title: Associations
 ---
 
-::: otg.datasource.gwas_catalog.associations.GWASCatalogAssociations
+::: otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser
+
+---
+
+::: otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog

docs/python_api/datasource/gwas_catalog/study_index.md

@@ -2,4 +2,8 @@
 title: Study Index
 ---
 
-::: otg.datasource.gwas_catalog.study_index.GWASCatalogStudyIndex
+::: otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser
+
+---
+
+::: otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog

docs/python_api/step/gwas_catalog.md

@@ -0,0 +1,5 @@
+---
+title: GWAS Catalog
+---
+
+::: otg.gwas_catalog_ingestion.GWASCatalogIngestionStep