name: genmap_mappability
description: create mappability file for a genome
keywords:
  - mappability
tools:
  - genmap:
      description: Ultra-fast computation of genome mappability.
      homepage: https://github.com/cpockrandt/genmap
      documentation: https://github.com/cpockrandt/genmap
      tool_dev_url: https://github.com/cpockrandt/genmap
      doi: "10.1093/bioinformatics/btaa222"
      licence: ["BSD-3-Clause"]

input:
  - fasta:
      type: file
      description: fasta file
      pattern: "*.{fasta,fa}"
  - index:
      type: file
      description: index file

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - wig:
      type: file
      description: genmap wig mappability file
      pattern: "*.wig"
  - bedgraph:
      type: file
      description: genmap bedgraph mappability file
      pattern: "*.bedgraph"
  - txt:
      type: file
      description: genmap text mappability file
      pattern: "*.txt"

authors:
  - "@jianhong"