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"