diff --git a/src/gentropy/gwas_catalog_ingestion.py b/src/gentropy/gwas_catalog_ingestion.py index 5dab5bf16..5a5461523 100644 --- a/src/gentropy/gwas_catalog_ingestion.py +++ b/src/gentropy/gwas_catalog_ingestion.py @@ -28,7 +28,7 @@ def __init__( catalog_ancestry_files: list[str], catalog_sumstats_lut: str, catalog_associations_file: str, - gnomad_variant_path: str, + variant_annotation_path: str, catalog_studies_out: str, catalog_associations_out: str, distance: int = WindowBasedClumpingStepConfig().distance, @@ -43,7 +43,7 @@ def __init__( catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog. catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table. catalog_associations_file (str): Raw GWAS catalog associations file. - gnomad_variant_path (str): Path to GnomAD variants. + variant_annotation_path (str): Path to GnomAD variants. catalog_studies_out (str): Output GWAS catalog studies path. catalog_associations_out (str): Output GWAS catalog associations path. distance (int): Distance, within which tagging variants are collected around the semi-index. @@ -51,7 +51,7 @@ def __init__( inclusion_list_path (str | None): optional inclusion list (parquet) """ # Extract - gnomad_variants = VariantIndex.from_parquet(session, gnomad_variant_path) + gnomad_variants = VariantIndex.from_parquet(session, variant_annotation_path) catalog_studies = session.spark.read.csv( list(catalog_study_files), sep="\t", header=True )