name: porechop
description: Adapter removal and demultiplexing of Oxford Nanopore reads
keywords:
  - adapter
  - nanopore
  - demultiplexing
tools:
  - porechop:
      description: Adapter removal and demultiplexing of Oxford Nanopore reads
      homepage: "https://github.com/rrwick/Porechop"
      documentation: "https://github.com/rrwick/Porechop"
      tool_dev_url: "https://github.com/rrwick/Porechop"
      doi: "10.1099/mgen.0.000132"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: fastq/fastq.gz file
      pattern: "*.{fastq,fastq.gz,fq,fq.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - reads:
      type: file
      description: Demultiplexed and/or adapter-trimmed fastq.gz file
      pattern: "*.{fastq.gz}"

authors:
  - "@ggabernet"
  - "@jasmezz"
  - "@d4straub"
  - "@LaurenceKuhl"
  - "@SusiJo"
  - "@jonasscheid"
  - "@jonoave"
  - "@GokceOGUZ"