name: abacas
description: contiguate draft genome assembly
keywords:
  - genome
  - assembly
  - contiguate
tools:
  - abacas:
      description: ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
      homepage: http://abacas.sourceforge.net/documentation.html
      documentation: http://abacas.sourceforge.net/documentation.html
      tool_dev_url: None
      doi: "10.1093/bioinformatics/btp347"
      licence: ['GPL v2-or-later']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - scaffold:
      type: file
      description: Fasta file containing scaffold
      pattern: "*.{fasta,fa}"
  - fasta:
      type: file
      description: FASTA reference file
      pattern: "*.{fasta,fa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - results:
      type: file
      description: Sorted BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

authors:
  - "@joseespinosa"
  - "@drpatelh"