From 029f3a512691a7e8ea0027705083768047b13c9f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:46:38 -0500
Subject: [PATCH] feat: Add PREDICTHAPLO module

---
 modules/predicthaplo/main.nf | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 modules/predicthaplo/main.nf

diff --git a/modules/predicthaplo/main.nf b/modules/predicthaplo/main.nf
new file mode 100644
index 0000000..71d2fc1
--- /dev/null
+++ b/modules/predicthaplo/main.nf
@@ -0,0 +1,23 @@
+process PREDICTHAPLO {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
+
+    input:
+    tuple val(prefix), path(bam)
+    path(reference)
+
+    output:
+    tuple val(prefix), path("*.fa*")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    """
+    predicthaplo \\
+        --sam "${bam}" \\
+        --reference "${reference}" \\
+        --prefix "${prefix}"
+    """
+}