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 ]
  - input:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - input_index:
      type: file
      description: BAM/CRAM/SAM index file
      pattern: "*.{bai,crai,sai}"
  - loci:
      type: file
      description: loci file <CHR><tab><POS1>
      pattern: "*.{tsv}"
  - fasta:
      type: file
      description: Input genome fasta file. Required when passing CRAM files.

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"
  - "@fbdtemme"