fix: properly write to log file in order_contigs rule

IKIM-Essen · Nov 6, 2024 · 373a3c4 · 373a3c4
1 parent 17b4f32
commit 373a3c4
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/rules/assembly.smk b/workflow/rules/assembly.smk
@@ -136,8 +136,8 @@ rule order_contigs:
     shadow:
         "minimal"
     shell:
-        " ragtag.py scaffold -C -w -o {params.outdir}/{wildcards.sample} {input.reference} {input.contigs} &&"
-        " mv {params.outdir}/{wildcards.sample}/ragtag.scaffold.fasta {output} > {log} 2>&1"
+        "(ragtag.py scaffold -C -w -o {params.outdir}/{wildcards.sample} {input.reference} {input.contigs} &&"
+        " mv {params.outdir}/{wildcards.sample}/ragtag.scaffold.fasta {output}) > {log} 2>&1"
 
 
 rule filter_chr0: