process HAPLINK_HAPLOTYPES {
    tag "${prefix}"
    label 'process_high'
    label 'haplink'

    container 'ghcr.io/ksumngs/haplink.jl:1.0.0'

    input:
    tuple val(prefix), path(bam), path(bai), path(vcf)
    path reference

    output:
    tuple val(prefix), path("*.yaml")

    publishDir "${params.outdir}/${task.process}", mode: 'copy'

    when:
    task.ext.when == null || task.ext.when

    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"
    """
}