name: cutadapt description: Perform adapter/quality trimming on sequencing reads keywords: - trimming - adapter trimming - adapters - quality trimming tools: - cuatadapt: description: | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: DOI:10.14806/ej.17.1.200 licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: The trimmed/modified fastq reads pattern: "*fastq.gz" - log: type: file description: cuatadapt log file pattern: "*cutadapt.log" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden"