process CLIQUESNV {
    tag "${prefix}"
    label 'process_high'
    label 'cliquesnv'

    container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0'

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

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

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

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

    script:
    def jmemstring = task.memory.toMega() + 'M'
    """
    cliquesnv \\
        -Xmx${jmemstring} \\
        -threads ${task.cpus} \\
        -m '${method}' \\
        -in "${bam}" \\
        -outDir .
    """
}