diff --git a/main.nf b/main.nf
index d107829..58335df 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,7 @@
 #!/usr/bin/env nextflow
 
+include { VIQUAS } from './modules/viquas'
+
 workflow {
 
     Channel
@@ -58,6 +60,11 @@ workflow {
         ch_all_haplotypes,
         ch_reference
     )
+
+    VIQUAS(
+        ch_alignments,
+        ch_reference
+    )
 }
 
 process EFETCH {