fix log not being found by the system

IKIM-Essen · Oct 27, 2024 · 3341251 · 3341251
1 parent 9cb1576
commit 3341251
Showing 1 changed file with 1 addition and 2 deletions.
diff --git 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: