From de853c2d229106ddcf99ef877ecb35cc012f35e8 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:40:04 -0500
Subject: [PATCH] feat: Add CliqueSNV module

---
 modules/cliquesnv/main.nf | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 modules/cliquesnv/main.nf

diff --git a/modules/cliquesnv/main.nf b/modules/cliquesnv/main.nf
new file mode 100644
index 0000000..f22ffa1
--- /dev/null
+++ b/modules/cliquesnv/main.nf
@@ -0,0 +1,27 @@
+process CLIQUESNV {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'
+
+    input:
+    tuple val(prefix), path(bam)
+    val(method)
+
+    output:
+    tuple val(prefix), path("*.json")
+    tuple val(prefix), path("*.fasta")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def jmemstring = task.memory.toMega() + 'M'
+    """
+    cliquesnv \\
+        -Xmx${jmemstring} \\
+        -threads ${task.cpus} \\
+        -m '${method}' \\
+        -in "${bam}" \\
+        -outDir .
+    """
+}