diff --git a/main.nf b/main.nf
index 65b1fd1..c73f49c 100755
--- a/main.nf
+++ b/main.nf
@@ -34,6 +34,11 @@ workflow {
         .out
         .set { ch_alignments }
 
+    CLIQUESNV(
+        ch_alignments,
+        'snv-pacbio'
+    )
+
     HAPLINK_VARIANTS( ch_alignments, ch_reference )
     HAPLINK_VARIANTS
         .out
@@ -75,9 +80,4 @@ workflow {
         ch_alignments,
         ch_reference
     )
-
-    CLIQUESNV(
-        ch_alignments,
-        'snv-pacbio'
-    )
 }