feat: updating step config file

src/gentropy/config.py

@@ -328,6 +328,24 @@ class WindowBasedClumpingStep(StepConfig):
     _target_: str = "gentropy.window_based_clumping.WindowBasedClumpingStep"
 
 
+@dataclass
+class FinemapperConfig(StepConfig):
+    """SuSiE fine-mapper step configuration."""
+
+    session: Any = field(
+        default_factory=lambda: {
+            "start_hail": True,
+        }
+    )
+    study_locus_to_finemap: str = MISSING
+    study_locus_collected_path: str = MISSING
+    study_index_path: str = MISSING
+    output_path: str = MISSING
+    locus_radius: int = MISSING
+    locus_l: int = MISSING
+    _target_: str = "gentropy.susie_finemapping.SusieFineMapperStep"
+
+
 @dataclass
 class Config:
     """Application configuration."""
@@ -385,3 +403,4 @@ def register_config() -> None:
     cs.store(group="step", name="variant_index", node=VariantIndexConfig)
     cs.store(group="step", name="variant_to_gene", node=VariantToGeneConfig)
     cs.store(group="step", name="window_based_clumping", node=WindowBasedClumpingStep)
+    cs.store(group="step", name="susie_finemapping", node=FinemapperConfig)

src/gentropy/susie_finemapper.py

@@ -36,7 +36,7 @@ def __init__(
         study_index_path: str,
         output_path: str,
         locus_radius: int = 500_000,
-        locus_L: int = 10,
+        locus_l: int = 10,
     ) -> None:
         """Run fine-mapping on a studyLocusId from a collected studyLocus table.
 
@@ -47,7 +47,7 @@ def __init__(
             study_index_path (str): path to the study index
             output_path (str): path to the output
             locus_radius (int): Radius of base-pair window around the locus, default is 500_000
-            locus_L (int): Maximum number of causal variants in locus, default is 10
+            locus_l (int): Maximum number of causal variants in locus, default is 10
         """
         # Read studyLocus
         study_locus = (
@@ -62,7 +62,7 @@ def __init__(
             study_locus,
             study_index,
             locus_radius * 2,
-            locus_L,
+            locus_l,
         )
         # Write result
         result.df.write.mode(session.write_mode).parquet(