From 444001b49931911958695cd201752b4971922f33 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:50:37 -0500
Subject: [PATCH] feat: Add QUASIRECOMB to pipeline

---
 main.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 8cf7dd2..4042eeb 100755
--- a/main.nf
+++ b/main.nf
@@ -8,7 +8,8 @@ include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
 include { HAPLINK_VARIANTS } from './modules/haplink/variants'
 include { PREDICTHAPLO } from './modules/predicthaplo'
 include { MINIMAP2 } from './modules/minimap2'
-include { NANOFILT } form './modules/nanofilt'
+include { NANOFILT } from './modules/nanofilt'
+include { QUASIRECOMB } from './modules/quasirecomb'
 include { SHORAH_AMPLICON } from './modules/shorah/amplicon'
 include { SHORAH_SHOTGUN } from './modules/shorah/shotgun'
 include { VIQUAS } from './modules/viquas'
@@ -82,6 +83,8 @@ workflow {
         ch_reference
     )
 
+    QUASIRECOMB( ch_alignments )
+
     VIQUAS(
         ch_alignments,
         ch_reference