name: allelecounter description: Generates a count of coverage of alleles keywords: - allele - count tools: - allelecounter: description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings) homepage: https://github.com/cancerit/alleleCount documentation: https://github.com/cancerit/alleleCount tool_dev_url: https://github.com/cancerit/alleleCount doi: "" licence: A-GPL 3.0 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - bai: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - loci: type: file description: loci file pattern: "*.{tsv}" 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" - alleleCount: type: file description: Allele count file pattern: "*.{alleleCount}" authors: - "@fullama"