diff --git a/workflow/main.nf b/workflow/main.nf
index 7fef409383c9ca5bca8dabe1b38949aeb21d79a1..71cb08c6c7088d163cbd8bfb4d8fe220b65a553b 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -36,7 +36,7 @@ process checkDesignFile {
 
   output:
 
-  file("design.csv") into designPaths
+  file("design.checked.csv") into designPaths
 
   script:
 
diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py
index 6c0246ac41fbf0acf89afbd438444f45addc7e12..f22217764b8417f8f75ad98e779084ee51ebd494 100755
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
@@ -100,7 +100,7 @@ def main():
     new_design_df = check_design_headers(design_df)
     check_files(design_df, fastq_df)
 
-    new_design_df.to_csv('design.csv', header=True, sep=',', index=False)
+    new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
 
 if __name__ == '__main__':
     main()