name: trimgalore description: Trim FastQ files using Trim Galore! keywords: - trimming - adapters - sequencing adapters - fastq tools: - trimgalore: description: | A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md 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: | List of input adapter trimmed FastQ files of size 1 and 2 for single-end and paired-end data, respectively. pattern: "*.{fq.gz}" - html: type: file description: FastQC report (optional) pattern: "*_{fastqc.html}" - zip: type: file description: FastQC report archive (optional) pattern: "*_{fastqc.zip}" - log: type: file description: Trim Galore! trimming report pattern: "*_{report.txt}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@drpatelh" - "@ewels" - "@FelixKrueger"