process VIQUAS {
    tag "${prefix}"
    label 'process_high'
    label 'viquas'

    container 'code.millironx.com/millironx/haplotyper-battle-royale:viquas'

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

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

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

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

    script:
    """
    viquas \\
        ${reference} \\
        ${bam}
    """
}