name: Trim Galore! description: Trim FastQ files using Trim Galore! keywords: - trimming - adapters - sequencing adapters tools: - fastqc: 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: - - sample_id: type: string description: Sample identifier - reads: type: file description: Input FastQ file, or pair of files output: - - sample_id: type: string description: Sample identifier - trimmed_fastq: type: file description: Trimmed FastQ files pattern: *fq.gz - - report: type: file description: Trim Galore! trimming report pattern: *trimming_report.txt authors: - - @ewels - @FelixKrueger