From ad10d46c877bbc4412099b31db59744b0365d0d4 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 8 Jun 2023 18:12:23 -0500
Subject: [PATCH] feat: Add SHORAH_SHOTGUN process

---
 main.nf | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/main.nf b/main.nf
index f6d5a5f..d107829 100755
--- a/main.nf
+++ b/main.nf
@@ -165,6 +165,29 @@ process SHORAH_AMPLICON {
     """
 }
 
+process SHORAH_SHOTGUN {
+    label 'process_high'
+    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.vcf")
+    tuple val(prefix), path("*support.fas")
+
+    publishDir "results/shorah-shotgun", mode: 'copy'
+
+    script:
+    """
+    shorah shotgun \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}
+
 process HAPLINK_VARIANTS {
     cpus 2
     memory '12.GB'