name: ucsc_liftover
description: convert between genome builds
keywords:
  - liftOver
tools:
  - ucsc:
      description: Move annotations from one assembly to another
      homepage: http://hgdownload.cse.ucsc.edu/admin/exe/
      documentation: None
      tool_dev_url: None
      doi: ""
      licence: ['varies; see http://genome.ucsc.edu/license']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: Browser Extensible Data (BED) file
      pattern: "*.{bed}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - lifted:
      type: file
      description: BED file containing successfully lifted variants
      pattern: "*.{lifted.bed}"
  - unlifted:
      type: file
      description: BED file containing variants that couldn't be lifted
      pattern: "*.{unlifted.bed}"

authors:
  - "@nebfield"