process cutadapt { tag "${sample_id}" container 'quay.io/biocontainers/cutadapt:1.16--py27_1' input: tuple val(sample_id), file(reads) output: tuple sample_id, file("trimmed_*.fastq") script: forward_fq = "trimmed_1.fastq" reverse_fq = "trimmed_2.fastq" if (params.singleEnd) { processing = """ cutadapt \ -j ${task.cpus} \ -q $params.cutadapt_min_quality \ --minimum-length $params.cutadapt_min_length \ --output ${forward_fq} \ ${reads} """ } else { processing = """ cutadapt \ -j ${task.cpus} \ -q $params.cutadapt_min_quality \ --minimum-length $params.cutadapt_min_length \ --pair-filter=any \ --output ${forward_fq} \ --paired-output ${reverse_fq} ${reads} """ } version = """ cutadapt --version &> v_cutadapt.txt """ return processing + version }