diff --git a/workflow/rules/assembly.smk b/workflow/rules/assembly.smk
index 5b81a807..f2783e78 100644
--- a/workflow/rules/assembly.smk
+++ b/workflow/rules/assembly.smk
@@ -136,7 +136,7 @@ rule order_contigs:
     shadow:
         "minimal"
     shell:
-        " ragtag.py scaffold -C -o {params.outdir}/{wildcards.sample} {input.reference} {input.contigs} &&"
+        " 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"