name: fastp
description: Perform adapter/quality trimming on sequencing reads
keywords:
  - trimming
  - quality control
  - fastq
tools:
  - fastq:
      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
params:
  - outdir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$params.outdir/<SOFTWARE>`
  - publish_dir_mode:
      type: string
      description: |
        Value for the Nextflow `publishDir` mode parameter.
        Available: symlink, rellink, link, copy, copyNoFollow, move.
  - enable_conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive
  - singularity_pull_docker_container:
      type: boolean
      description: |
        Instead of directly downloading Singularity images for use with Singularity,
        force the workflow to pull and convert Docker containers instead.

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"