From 5ab64a8feab2c283eb881a6714e3ac88521ccf2b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:43:02 -0500
Subject: [PATCH] feat: Add CliqueSNV haplotype calling to pipeline

---
 main.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/main.nf b/main.nf
index e623fa6..65b1fd1 100755
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,6 @@
 #!/usr/bin/env nextflow
 
+include { CLIQUESNV } from './modules/cliquesnv'
 include { EFETCH } from './modules/efetch'
 include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
 include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
@@ -74,4 +75,9 @@ workflow {
         ch_alignments,
         ch_reference
     )
+
+    CLIQUESNV(
+        ch_alignments,
+        'snv-pacbio'
+    )
 }