From 9198d1186c10efdc12dc3e92c63c80d688a235e5 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 9 Aug 2023 16:09:55 -0500
Subject: [PATCH] feat: Add ViQuas to main pipeline

---
 main.nf | 7 +++++++
 1 file changed, 7 insertions(+)

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 {