diff --git a/conf/modules.config b/conf/modules.config
index 23f177c..16cc46c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -192,11 +192,13 @@ process {
     }
 }
 
-process {
-    withName: '.*:PREPARE_REFERENCE_FILES:PREPARE_GTF' {
-        publishDir = [
-            enabled: false
-        ]
+if (params.intron_retention_method){
+    process {
+        withName: '.*:PREPARE_REFERENCE_FILES:PREPARE_GTF' {
+            publishDir = [
+                enabled: false
+            ]
+        }
     }
 }