name: gffread
description: Validate, filter, convert and perform various other operations on GFF files
keywords:
  - gff
  - conversion
  - validation
tools:
  - gffread:
      description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
      homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
      documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
      tool_dev_url: https://github.com/gpertea/gffread
      doi: 10.12688/f1000research.23297.1
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gff:
        type: file
        description: A GFF file in either the GFF3 or GFF2 format.
        patter: "*.gff"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gtf:
      type: file
      description: GTF file resulting from the conversion of the GFF input file
      pattern: "*.gtf"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

authors:
  - "@emiller88"