name: nanolyse
description: DNA contaminant removal using NanoLyse
keywords:
  - contaminant_removal
tools:
  - nanolyse:
      description: |
        DNA contaminant removal using NanoLyse
      homepage: https://github.com/wdecoster/nanolyse
      documentation: https://github.com/wdecoster/nanolyse#nanolyse
      licence: ["GPL-3.0-or-later"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description: |
        Basecalled reads in FASTQ.GZ format
      pattern: "*.fastq.gz"
  - fasta:
      type: file
      description: |
        A reference fasta file against which to filter.
      pattern: "*.fasta"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description: Reads with contaminants removed in FASTQ format
      pattern: "*.fastq.gz"
  - log:
      type: file
      description: Log of the Nanolyse run.
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@yuukiiwa"