haplotyper-battle-royale/modules/minimap2/main.nf

process MINIMAP2 {
    tag "${prefix}"
    label 'process_medium'

    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'

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

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

    output:
    tuple val(prefix), path("*.bam"), path("*.bam.bai")
    script:
    """
    minimap2 \\
            -x map-ont \\
            --MD \\
            --eqx \\
            -t ${task.cpus} \\
            -a \\
            "${reference}" \\
            "${reads}" \\
    | samtools sort \\
    | samtools view \\
            -@ ${task.cpus} \\
            -b \\
            -h \\
            -o "${prefix}.bam"
    samtools index "${prefix}.bam"
    """
}