name: fastqc
description: Run FastQC on sequenced reads
keywords:
  - quality control
  - qc
  - adapters
  - fastq
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/
      licence: ["GPL-2.0-only"]
      identifier: biotools:fastqc
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:
  - html:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.html":
          type: file
          description: FastQC report
          pattern: "*_{fastqc.html}"
  - zip:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.zip":
          type: file
          description: FastQC report archive
          pattern: "*_{fastqc.zip}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@grst"
  - "@ewels"
  - "@FelixKrueger"
maintainers:
  - "@drpatelh"
  - "@grst"
  - "@ewels"
  - "@FelixKrueger"
