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chore: drop redundant parameter from sumstat qc step #802

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Merged
DSuveges merged 1 commit into from
Oct 1, 2024
Merged

chore: drop redundant parameter from sumstat qc step #802

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1 change: 0 additions & 1 deletion src/gentropy/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -439,7 +439,6 @@ class GWASQCStep(StepConfig):

gwas_path: str = MISSING
output_path: str = MISSING
studyid: str = MISSING
pval_threshold: float = MISSING
_target_: str = "gentropy.sumstat_qc_step.SummaryStatisticsQCStep"

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4 changes: 1 addition & 3 deletions src/gentropy/sumstat_qc_step.py
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Expand Up @@ -15,7 +15,6 @@ def __init__(
session: Session,
gwas_path: str,
output_path: str,
studyid: str,
pval_threshold: float = 1e-8,
) -> None:
"""Calculating quality control metrics on the provided GWAS study.
Expand All @@ -24,7 +23,6 @@ def __init__(
session (Session): Spark session
gwas_path (str): Path to the GWAS summary statistics.
output_path (str): Output path for the QC results.
studyid (str): Study ID for the QC.
pval_threshold (float): P-value threshold for the QC. Default is 1e-8.

"""
Expand All @@ -35,5 +33,5 @@ def __init__(
gwas=gwas, limit=100_000_000, pval_threshold=pval_threshold
)
.write.mode(session.write_mode)
.parquet(output_path + "/qc_results_" + studyid)
.parquet(output_path)
)