diff --git a/config/datasets/ot_gcp.yaml b/config/datasets/ot_gcp.yaml index 8f4243bb6..09cece996 100644 --- a/config/datasets/ot_gcp.yaml +++ b/config/datasets/ot_gcp.yaml @@ -31,7 +31,7 @@ gwas_catalog_study_locus_folder: ${datasets.gwas_catalog_dataset}/study_locus_da gwas_catalog_credible_set_folder: ${datasets.gwas_catalog_dataset}/credible_set_datasets # GnomAD -gnomad_public_bucket: gs://gcp-public-data--gnomad/release +gnomad_public_bucket: gs://gcp-public-data--gnomad/release/ # LD generation # Templates require placeholders {POP} to expand template to match multiple populationwise paths ld_matrix_template: ${datasets.gnomad_public_bucket}/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm @@ -61,7 +61,7 @@ summary_statistics: ${datasets.outputs}/summary_statistics study_locus_overlap: ${datasets.outputs}/study_locus_overlap susie_finemapping: ${datasets.outputs}/finngen_susie_finemapping -ld_index: ${datasets.outputs}/ld_index +ld_index: ${datasets.static_assets}/ld_index catalog_study_index: ${datasets.study_index}/catalog catalog_study_locus: ${datasets.study_locus}/catalog_study_locus diff --git a/config/step/ot_ld_based_clumping.yaml b/config/step/ot_ld_based_clumping.yaml index d02c0acdd..f836145c2 100644 --- a/config/step/ot_ld_based_clumping.yaml +++ b/config/step/ot_ld_based_clumping.yaml @@ -1,7 +1,7 @@ defaults: - ld_based_clumping -ld_index_path: ${datasets.ld_index} +ld_index_path: ${datasets.ld_index}/2.1.1 study_locus_input_path: ??? study_index_path: ??? clumped_study_locus_output_path: ??? diff --git a/config/step/ot_ld_index.yaml b/config/step/ot_ld_index.yaml index e72711618..d17a0777c 100644 --- a/config/step/ot_ld_index.yaml +++ b/config/step/ot_ld_index.yaml @@ -4,7 +4,7 @@ defaults: ld_index_out: ${datasets.ld_index} ld_matrix_template: ${datasets.ld_matrix_template} ld_index_raw_template: ${datasets.ld_index_raw_template} -grch37_to_grch38_chain_path: ${datasets.chain_37_38.} +grch37_to_grch38_chain_path: ${datasets.chain_37_38} liftover_ht_path: ${datasets.liftover_ht_path} ld_populations: - afr # African-American diff --git a/src/gentropy/ld_index.py b/src/gentropy/ld_index.py index 3941d5c02..0cc00cf14 100644 --- a/src/gentropy/ld_index.py +++ b/src/gentropy/ld_index.py @@ -29,6 +29,7 @@ def __init__( ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template, ld_populations: list[LD_Population | str] = LDIndexConfig().ld_populations, liftover_ht_path: str = LDIndexConfig().liftover_ht_path, + grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path, use_version_from_input: bool = LDIndexConfig().use_version_from_input, ) -> None: """Run step. @@ -41,6 +42,7 @@ def __init__( ld_index_raw_template (str): Input path to the raw gnomAD LD indices file with placeholder for population string ld_populations (list[LD_Population | str]): Population names derived from the ld file paths liftover_ht_path (str): Path to the liftover ht file + grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates. use_version_from_input (bool): Append version derived from input ld_matrix_template to the output ld_index_out. Defaults to False. In case use_version_from_input is set to True, @@ -57,6 +59,7 @@ def __init__( GnomADLDMatrix( ld_matrix_template=ld_matrix_template, ld_index_raw_template=ld_index_raw_template, + grch37_to_grch38_chain_path=grch37_to_grch38_chain_path, ld_populations=ld_populations, liftover_ht_path=liftover_ht_path, )