feat: Add CliqueSNV module

2023-09-23 16:40:04 -05:00 · 2023-09-23 16:40:04 -05:00 · de853c2d22
commit de853c2d22
parent 5c4d02263b
1 changed files with 27 additions and 0 deletions
--- a/modules/cliquesnv/main.nf
+++ 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 .
+    """
+}