From 00772f8010e5273cde28ee68c8aff1eb308ac741 Mon Sep 17 00:00:00 2001 From: KIESER Silas Date: Mon, 15 Jan 2024 09:30:54 +0100 Subject: [PATCH] fix error of contaminants --- workflow/rules/qc.smk | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index 985e72e7..0dcb7401 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -314,12 +314,10 @@ if not SKIP_QC: ) ), stats="{sample}/sequence_quality_control/{sample}_decontamination_reference_stats.txt", + contaminant_folder= directory("Intermediate/qc/decontamination/{sample}") benchmark: "logs/benchmarks/QC/decontamination/{sample}.txt" params: - contaminant_folder=lambda wc, output: os.path.dirname( - output.contaminants[0] - ), maxindel=config["contaminant_max_indel"], minratio=config["contaminant_min_ratio"], minhits=config["contaminant_minimum_hits"], @@ -345,7 +343,7 @@ if not SKIP_QC: " bbsplit.sh " " {params.inputs} " " {params.outputs} " - " basename={params.contaminant_folder}/%_R#.fastq.gz " + " basename={output.contaminant_folder}/%_R#.fastq.gz " " maxindel={params.maxindel} " " minratio={params.minratio} " " minhits={params.minhits} "