feat: Add new HAPLINK_HAPLOTYPES module

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"
+    """
+}