diff --git a/main.nf b/main.nf
index 4042eeb..af776f3 100755
--- a/main.nf
+++ b/main.nf
@@ -85,6 +85,16 @@ workflow {
 
     QUASIRECOMB( ch_alignments )
 
+    SHORAH_AMPLICON(
+        ch_alignments,
+        ch_reference
+    )
+
+    SHORAH_SHOTGUN(
+        ch_alignments,
+        ch_reference
+    )
+
     VIQUAS(
         ch_alignments,
         ch_reference