diff --git a/src/otg/clump.py b/src/otg/clump.py index 8cb756fa0..c8b587126 100644 --- a/src/otg/clump.py +++ b/src/otg/clump.py @@ -45,7 +45,9 @@ def __post_init__(self: ClumpStep) -> None: Raises: ValueError: If study index and LD index paths are not provided for study locus. """ - input_cols = self.session.spark.read.parquet(self.input_path).columns + input_cols = self.session.spark.read.parquet( + self.input_path, recursiveFileLookup=True + ).columns if "studyLocusId" in input_cols: if self.study_index_path is None or self.ld_index_path is None: raise ValueError( @@ -59,7 +61,9 @@ def __post_init__(self: ClumpStep) -> None: study_index=study_index, ld_index=ld_index ).clump() else: - sumstats = SummaryStatistics.from_parquet(self.session, self.input_path) + sumstats = SummaryStatistics.from_parquet( + self.session, self.input_path, recursiveFileLookup=True + ) clumped_study_locus = sumstats.window_based_clumping( locus_collect_distance=self.locus_collect_distance )