process HAPLINK_SEQUENCES {
    tag "${method}: ${prefix}"
    label 'process_single'
    label 'haplink'

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

    input:
    tuple val(prefix), val(method), path(yaml)
    path reference

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

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

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

    script:
    """
    export JULIA_NUM_THREADS=${task.cpus}
    haplink sequences \\
            "${reference}" \\
            "${yaml}" \\
            --prefix "${prefix}" \\
        > "${prefix}.fasta"
    """
}