name: bcftools_merge
description: Merge VCF files
keywords:
  - variant calling
  - merge
  - VCF
tools:
  - merge:
      description: |
        Merge VCF files.
      homepage: http://samtools.github.io/bcftools/bcftools.html
      documentation: http://www.htslib.org/doc/bcftools.html
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcfs:
      type: file
      description: |
        List containing 2 or more vcf files
        e.g. [ 'file1.vcf', 'file2.vcf' ]
  - tbis:
      type: file
      description: |
        List containing the tbi index files corresponding to the vcfs input files
        e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)"
      pattern: "*.{fasta,fa}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)"
      pattern: "*.fai"
  - bed:
      type: file
      description: "(Optional) The bed regions to merge on"
      pattern: "*.bed"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf_gz:
      type: file
      description: VCF merged output file (bgzipped) => when `--output-type z` is used
      pattern: "*.vcf.gz"
  - vcf:
      type: file
      description: VCF merged output file => when `--output-type v` is used
      pattern: "*.vcf"
  - bcf_gz:
      type: file
      description: BCF merged output file (bgzipped) => when `--output-type b` is used
      pattern: "*.bcf.gz"
  - bcf:
      type: file
      description: BCF merged output file => when `--output-type u` is used
      pattern: "*.bcf"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
  - "@nvnieuwk"
  - "@ramprasadn"
