name: hmmcopy_generatemap
description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
keywords:
  - hmmcopy
  - mapcounter
  - mappability
tools:
  - hmmcopy:
      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
      homepage: https://github.com/shahcompbio/hmmcopy_utils
      documentation: https://github.com/shahcompbio/hmmcopy_utils
      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
      doi: ""
      licence: ["GPL v3"]

input:
  - fasta:
      type: file
      description: Input genome fasta file

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bigwig:
      type: file
      description: bigwig file containing the mappability of the genome
      pattern: "*.{map.bw}"

authors:
  - "@sppearce"