name: freebayes
description: A haplotype-based variant detector
keywords:
  - variant caller
  - SNP
  - genotyping
  - somatic variant calling
  - germline variant calling
  - bacterial variant calling
  - bayesian

tools:
  - freebayes:
      description: Bayesian haplotype-based polymorphism discovery and genotyping
      homepage: https://github.com/freebayes/freebayes
      documentation: https://github.com/freebayes/freebayes
      tool_dev_url: https://github.com/freebayes/freebayes
      doi: "arXiv:1207.3907"
      licence: ['MIT']

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: "*.bam.bai"
  - fasta:
      type: file
      description: reference fasta file
      pattern: ".{fa,fa.gz,fasta,fasta.gz}"
  - fasta_fai:
      type: file
      description: reference fasta file index
      pattern: "*.{fa,fasta}.fai"
  - targets:
      type: file
      description: Optional - Limit analysis to targets listed in this BED-format FILE.
      pattern: "*.bed"
  - samples:
      type: file
      description: Optional - Limit analysis to samples listed (one per line) in the FILE.
      pattern: "*.txt"
  - populations:
      type: file
      description: Optional - Each line of FILE should list a sample and a population which it is part of.
      pattern: "*.txt"
  - cnv:
      type: file
      description: |
          A copy number map BED file, which has either a sample-level ploidy:
          sample_name copy_number
          or a region-specific format:
          seq_name start end sample_name copy_number
      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: "*.{version.txt}"
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.vcf.gz"

authors:
  - "@maxibor"
  - "@FriederikeHanssen"
  - "@maxulysse"