name: filtlong
description: Filtlong filters long reads based on quality measures or short read data.
keywords:
  - nanopore
  - quality control
  - QC
  - filtering
  - long reads
  - short reads
tools:
  - filtlong:
      description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
      homepage: https://anaconda.org/bioconda/filtlong
      documentation: None
      tool_dev_url: https://github.com/rrwick/Filtlong
      doi: ""
      licence: ["GPL v3"]

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

authors:
  - "@d4straub"