From 3341251331173b7a73f67e2a382139ac142a4885 Mon Sep 17 00:00:00 2001 From: Hamdiye Uzuner Date: Sun, 27 Oct 2024 22:34:14 +0100 Subject: [PATCH] fix log not being found by the system --- workflow/rules/read_clipping.smk | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk index bc41c220..9c693e82 100644 --- a/workflow/rules/read_clipping.smk +++ b/workflow/rules/read_clipping.smk @@ -44,7 +44,6 @@ rule bamclipper: ), params: output_dir=get_output_dir, - cwd=lambda w: os.getcwd(), bed_path=lambda w, input: os.path.join(os.getcwd(), input.bedpe), bam=lambda w, input: os.path.basename(input.bam), log: @@ -57,7 +56,7 @@ rule bamclipper: " cp {input.bai} {params.output_dir} &&" " cd {params.output_dir} &&" " bamclipper.sh -b {params.bam} -p {params.bed_path} -n {threads} -u 5 -d 5) " - " > {params.cwd}/{log} 2>&1" + " > {log} 2>&1" rule fgbio: