haplotyper-battle-royale/modules/quasirecomb/main.nf

process QUASIRECOMB {
    tag "${prefix}"
    label 'process_high'
    label 'quasirecomb'

    container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'

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

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

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

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

    script:
    def jmemstring = task.memory.toMega() + 'M'
    """
    quasirecomb \\
        -XX:+UseParallelGC \\
        -Xms2g \\
        -Xmx${jmemstring} \\
        -XX:+UseNUMA \\
        -XX:NewRatio=9 \\
        -i "${bam}"
    mv quasispecies.fasta "${prefix}.fasta"
    """
}