name: FastQC
description: Run FastQC on sequenced reads
keywords:
  - Quality Control
  - QC
  - Adapters
tools:
  - fastqc:
      description: |
        FastQC gives general quality metrics about your reads.
        It provides information about the quality score distribution
        across your reads, the per base sequence content (%A/C/G/T).
        You get information about adapter contamination and other
        overrepresented sequences.
      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
params:
  - fastqc_args:
      type: string
      description: Additional command line arguments passed to fastqc.
  - out_dir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$out_dir/MODULE_NAME`
  - publish_dir:
      type: string
      description: |
        Append to the path for the standard output directory provided by `$out_dir`.
  - publish_dir_mode:
      type: string
      description: |
        Provide a value for the Nextflow `publishDir` mode parameter
        (e.g. copy, link, ...)
  - publish_results:
      type: string
      description: |
        Whether or not to publish results into `publish_dir`. Set to `none` to not
        publish any files at all; to `default` to publish all relevant files.
input:
  - name:
      type: string
      description: Sample identifier
  - single_end:
      type: boolean
      description: |
        Boolean indicating whether the corresponding sample is single-end (true)
        or paired-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:
  - report:
      type: file
      description: FastQC report
      pattern: "*_fastqc.{zip,html}"
authors:
  - "@grst"
  - "@drpatelh"
  - "@ewels"
  - "@FelixKrueger"