process FLASH { tag "$meta.id" label 'process_medium' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5' : 'quay.io/biocontainers/flash:1.2.11--hed695b0_5' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("*.fastq.gz"), emit: reads path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ flash \\ $args \\ -o ${prefix} \\ -z \\ ${reads[0]} \\ ${reads[1]} cat <<-END_VERSIONS > versions.yml "${task.process}": flash: \$(echo \$(flash --version 2>&1) | sed 's/^.*FLASH v//; s/ .*\$//') END_VERSIONS """ }