From 47500bc9867d93d3b67f5358621da90552baf905 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:20:44 -0500
Subject: [PATCH] feat: Add new HAPLINK_HAPLOTYPES module

---
 modules/haplink/haplotypes/main.nf | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 modules/haplink/haplotypes/main.nf

diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
new file mode 100644
index 0000000..e4b96e8
--- /dev/null
+++ b/modules/haplink/haplotypes/main.nf
@@ -0,0 +1,28 @@
+process HAPLINK_HAPLOTYPES {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+
+    input:
+    tuple val(prefix), path(bam), path(bai)
+    path reference
+
+    output:
+    tuple val(prefix), path("*.yaml")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def ml_args = task.ext.ml_args ?: ''
+    """
+    export JULIA_NUM_THREADS=${task.cpus}
+    haplink haplotypes \\
+            "${reference}" \\
+            "${vcf}" \\
+            "${bam}" \\
+        --frequency 0.01 \\
+        ${ml_args} \\
+        > "${prefix}.yaml"
+    """
+}