process CUTADAPT { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : 'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1' }" input: tuple val(meta), path(reads) output: tuple val(meta), path('*.trim.fastq.gz'), emit: reads tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def trimmed = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz" """ cutadapt \\ --cores $task.cpus \\ $args \\ $trimmed \\ $reads \\ > ${prefix}.cutadapt.log cat <<-END_VERSIONS > versions.yml "${task.process}": cutadapt: \$(cutadapt --version) END_VERSIONS """ }