name: bbmap_bbduk description: Adapter and quality trimming of sequencing reads keywords: - trimming - adapter trimming - quality trimming tools: - bbmap: description: BBMap is a short read aligner, as well as various other bioinformatic tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" licence: ['UC-LBL license (see package)'] 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. - contaminants: type: file description: | Reference files containing adapter and/or contaminant sequences for sequence kmer matching 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" - versions: type: file description: File containing software versions pattern: "versions.yml" - log: type: file description: Bbduk log file pattern: "*bbduk.log" authors: - "@MGordon09"