From feb051fc07a9886617437491c24ee0f4de872995 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 8 Jun 2023 18:10:26 -0500
Subject: [PATCH] feat: Add SHORAH_AMPLICON process

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

diff --git a/main.nf b/main.nf
index 847d5dc..f6d5a5f 100755
--- a/main.nf
+++ b/main.nf
@@ -142,6 +142,29 @@ process MINIMAP2 {
     """
 }
 
+process SHORAH_AMPLICON {
+    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-amplicon", mode: 'copy'
+
+    script:
+    """
+    shorah amplicon \\
+        -t ${task.cpus} \\
+        -f ${reference} \\
+        -b ${bam} \\
+    """
+}
+
 process HAPLINK_VARIANTS {
     cpus 2
     memory '12.GB'