name: expansionhunter description: Estimate repeat sizes using NGS data keywords: - STR - repeat_expansions tools: - expansionhunter: description: A tool for estimating repeat sizes homepage: https://github.com/Illumina/ExpansionHunter documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md tool_dev_url: None doi: "10.1093/bioinformatics/btz431" licence: ["Apache-2.0"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" - fasta: type: file description: Reference genome pattern: "*.{fa,fasta}" - variant_catalog: type: file description: json file with repeat expansion sites to genotype pattern: "*.{json}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', gender:'female' ] - versions: type: file description: File containing software versions pattern: "versions.yml" - vcf: type: file description: VCF with repeat expansions pattern: "*.{vcf}" authors: - "@jemten"