name: cutadapt
description: Perform adapter/quality trimming on sequencing reads
keywords:
  - trimming
  - adapter trimming
  - adapters
  - quality trimming
tools:
  - cuatadapt:
      description: |
        Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
      documentation: https://cutadapt.readthedocs.io/en/stable/index.html
      doi: 10.14806/ej.17.1.200
      licence: ["MIT"]
      identifier: biotools:cutadapt
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:
  - reads:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.trim.fastq.gz":
          type: file
          description: The trimmed/modified fastq reads
          pattern: "*fastq.gz"
  - log:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.log":
          type: file
          description: cuatadapt log file
          pattern: "*cutadapt.log"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@kevinmenden"
maintainers:
  - "@drpatelh"
  - "@kevinmenden"
