diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index 2414cbd7ec897100ba9f4b19975239f0f841c405..6b673bb128143d810ca4cf6a5c09767a1be0b524 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -25,6 +25,6 @@ process gffread {
     file_prefix = file_id
   }
   """
-  gffread ${gtf} -g ${fasta} -o ${file_prefix}.fasta
+  gffread ${gtf} -g ${fasta} -x -o ${file_prefix}.fasta
   """
 }
\ No newline at end of file