name: bcftools_concat
description: Concatenate VCF files
keywords:
    - variant calling
    - concat
    - bcftools
    - VCF

tools:
    - concat:
        description: |
          Concatenate 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: files
        description: |
          List containing 2 or more vcf files
          e.g. [ 'file1.vcf', 'file2.vcf' ]
output:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - vcf:
        type: file
        description: VCF concatenated output file
        pattern: "*.{vcf.gz}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@abhi18av"