feat(config): 24.06 data release fixes (#639)

* feat(config): typos fix * fix(config): moved ld_index dataset to static assets --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
opentargets · Jun 13, 2024 · 3c8ce58 · 3c8ce58
1 parent 976ee30
commit 3c8ce58
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Showing 4 changed files with 7 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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,
             )