process SHORAH_AMPLICON {
    tag "${prefix}"
    label 'process_high'
    label 'shorah'

    container 'quay.io/biocontainers/shorah:1.99.2--py38h73782ee_8'

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

    output:
    tuple val(prefix), path("*.vcf")
    tuple val(prefix), path("*support.fas")

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

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

    script:
    """
    shorah amplicon \\
        -f ${reference} \\
        -b ${bam} \\
    """
}