From 3e6a0ca5df0caab7d99b32448d398e739dfbec63 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 23 Sep 2023 16:54:49 -0500
Subject: [PATCH] feat: Add QuasiRecomb module

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

diff --git a/modules/quasirecomb/main.nf b/modules/quasirecomb/main.nf
new file mode 100644
index 0000000..e2896c0
--- /dev/null
+++ b/modules/quasirecomb/main.nf
@@ -0,0 +1,27 @@
+process QUASIRECOMB {
+    tag "${prefix}"
+    label 'process_high'
+
+    container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
+
+    input:
+    tuple val(prefix), path(bam)
+
+    output:
+    tuple val(prefix), path("*.fasta")
+
+    publishDir "results/${task.process}", mode: 'copy'
+
+    script:
+    def jmemstring = task.memory.toMega() + 'M'
+    """
+    quasirecomb \\
+        -XX:+UseParallelGC \\
+        -Xms2g \\
+        -Xmx${jmemstring} \\
+        -XX:+UseNUMA \\
+        -XX:NewRatio=9 \\
+        -i "${bam}"
+    mv quasispecies.fasta "${prefix}.fasta"
+    """
+}