name: stranger description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes. keywords: - STR - repeat_expansions - annotate - vcf tools: - stranger: description: Annotate VCF files with str variants homepage: https://github.com/moonso/stranger documentation: https://github.com/moonso/stranger tool_dev_url: https://github.com/moonso/stranger doi: "10.5281/zenodo.4548873" licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: VCF with repeat expansions pattern: "*.{vcf.gz,vcf}" 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" - vcf: type: file description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin pattern: "*.{vcf.gz}" authors: - "@ljmesi"