diff --git a/modules/cnvkit/reference/main.nf b/modules/cnvkit/reference/main.nf
index d5b8baa0..10458f27 100644
--- a/modules/cnvkit/reference/main.nf
+++ b/modules/cnvkit/reference/main.nf
@@ -21,7 +21,7 @@ process CNVKIT_REFERENCE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: targets.BaseName
 
     """
     cnvkit.py \\
diff --git a/tests/modules/cnvkit/reference/test.yml b/tests/modules/cnvkit/reference/test.yml
index b1b8c896..a5baf0a2 100644
--- a/tests/modules/cnvkit/reference/test.yml
+++ b/tests/modules/cnvkit/reference/test.yml
@@ -4,5 +4,5 @@
     - cnvkit/reference
     - cnvkit
   files:
-    - path: output/cnvkit/reference.cnn
+    - path: output/cnvkit/multi_intervals.reference.cnn
       md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9