name: fastp description: Perform adapter/quality trimming on sequencing reads keywords: - trimming - quality control - fastq tools: - fastp: description: | A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. documentation: https://github.com/OpenGene/fastp doi: https://doi.org/10.1093/bioinformatics/bty560 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: "*trim.fastq.gz" - json: type: file description: Results in JSON format pattern: "*.json" - html: type: file description: Results in HTML format pattern: "*.thml" - log: type: file description: fastq log file pattern: "*.log" - version: type: file description: File containing software version pattern: "*.{version.txt}" - reads_fail: type: file description: Reads the failed the preprocessing pattern: "*fail.fastq.gz" authors: - "@drpatelh" - "@kevinmenden"