diff --git a/workflow/main.nf b/workflow/main.nf
index 04b47a045896f19eba9b55aff3fe58d592ae68cf..14e48130d77c2b77f5adb30b9a29b7d45ab01099 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -64,6 +64,8 @@ process cr_count {
             noBam = "--no-bam"
         else
             noBam = ""
+
+        introns = introns.toLowerCase()
         
         // Run Cell Ranger count
         """