process PREDICTHAPLO {
    tag "${prefix}"
    label 'process_high'
    label 'predicthaplo'

    container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'

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

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

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

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

    script:
    """
    predicthaplo \\
        --sam "${bam}" \\
        --reference "${reference}" \\
        --prefix "${prefix}"
    """
}