name: pairix
description: |
    a tool for indexing and querying on a block-compressed text file
    containing pairs of genomic coordinates
keywords:
  - index
tools:
  - pairix:
      description: 2D indexing on bgzipped text files of paired genomic coordinates
      homepage: "https://github.com/4dn-dcic/pairix"
      documentation: "https://github.com/4dn-dcic/pairix"
      tool_dev_url: "https://github.com/4dn-dcic/pairix"
      doi: ""
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - pair:
      type: file
      description: pair file

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"
  - index:
      type: file
      description: pair index file
      pattern: "*.px2"

authors:
  - "@jianhong"