process MINIMAP2 { tag "${prefix}" cpus 4 memory '8.GB' container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' input: tuple val(prefix), path(reads) path reference publishDir "results", 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" """ }