From 355ce9a00a04722173b398a77d0286b5ee57b63f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:51:58 -0500
Subject: [PATCH] feat: Add SHORAH processes to pipeline

---
 main.nf | 10 ++++++++++
 1 file changed, 10 insertions(+)

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