From f7a73963e30f60111a7e138fb875f20708d460b4 Mon Sep 17 00:00:00 2001 From: rajwanir2 Date: Fri, 16 Aug 2024 14:41:49 -0400 Subject: [PATCH] Correcting conditions such with BCF input intensity and contamination check is default --- src/cgr_gwas_qc/workflow/Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cgr_gwas_qc/workflow/Snakefile b/src/cgr_gwas_qc/workflow/Snakefile index 92fccd24..1aa2a824 100644 --- a/src/cgr_gwas_qc/workflow/Snakefile +++ b/src/cgr_gwas_qc/workflow/Snakefile @@ -48,7 +48,7 @@ use rule * from sample_qc targets.extend(sample_qc.targets) -if sample_qc.use_contamination: +if sample_qc.use_contamination or cfg.config.user_files.bcf: module contamination: snakefile: @@ -61,7 +61,7 @@ if sample_qc.use_contamination: targets.extend(contamination.targets) -if sample_qc.use_contamination: +if sample_qc.use_contamination or cfg.config.user_files.bcf: module intensity_check: snakefile: