From a5588ae6fa27b28809a63e5dce63d3164e94a9a9 Mon Sep 17 00:00:00 2001 From: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Date: Tue, 1 Oct 2024 13:09:04 +0200 Subject: [PATCH] chore: drop redundant parameter (#802) Co-authored-by: Szymon Szyszkowski --- src/gentropy/config.py | 1 - src/gentropy/sumstat_qc_step.py | 4 +--- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/src/gentropy/config.py b/src/gentropy/config.py index 6f94cc9ed..33865d6ea 100644 --- a/src/gentropy/config.py +++ b/src/gentropy/config.py @@ -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" diff --git a/src/gentropy/sumstat_qc_step.py b/src/gentropy/sumstat_qc_step.py index b5aed905e..333ab19f3 100644 --- a/src/gentropy/sumstat_qc_step.py +++ b/src/gentropy/sumstat_qc_step.py @@ -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. @@ -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. """ @@ -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) )