diff --git a/workflow/main.nf b/workflow/main.nf
index 41a4a5ddebb02b0ffcaebc92be538454e896e35c..5ceaf89b59b06e5d4709556b5c17607ff2ed3883 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -50,7 +50,7 @@ process checkdesignfile {
 	script:
 	"""
   # convert dos \r to unix format
-  sed -i 's/\\x0D$//' design.ori.txt
+  sed -i 's/\\x0D\$//' design.ori.txt
 	bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
 	"""
 }