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/unmerged 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"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - reads_fail:
      type: file
      description: Reads the failed the preprocessing
      pattern: "*fail.fastq.gz"
  - reads_merged:
      type: file
      description: Reads that were successfully merged
      pattern: "*.{merged.fastq.gz}"
authors:
  - "@drpatelh"
  - "@kevinmenden"