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

process NANOFILT {
    tag "${prefix}"
    cpus 1
    memory '8.GB'
    container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'

    input:
    tuple val(prefix), path(reads)

    output:
    tuple val(prefix), path("*_trimmed.fastq.gz")

    script:
    """
    gzip \\
            -cdf "${reads}" \\
        | NanoFilt \\
            --logfile "trimmed/${prefix}.nanofilt.log" \\
            --length 100 \\
            --quality 7 \\
            --headcrop 30 \\
            --tailcrop 30 \\
            --minGC 0.1 \\
            --maxGC 0.9 \\
        | gzip \\
        > "${prefix}_trimmed.fastq.gz"
    """
}