process CLIQUESNV { tag "${prefix}" label 'process_high' label 'cliquesnv' container 'quay.io/biocontainers/cliquesnv:2.0.3--hdfd78af_0' input: tuple val(prefix), path(bam), path(bai) val(method) output: tuple val(prefix), path("*.json") tuple val(prefix), path("*.fasta") publishDir "results/${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 . """ }