name: glnexus
description: merge gVCF files and perform joint variant calling
keywords:
  - merge
  - gvcf
tools:
  - glnexus:
      description: scalable gVCF merging and joint variant calling for population sequencing projects.
      homepage: https://github.com/dnanexus-rnd/GLnexus
      documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
      tool_dev_url: None
      doi: https://doi.org/10.1101/343970
      licence: ["Apache-2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - gvcfs:
      type: list
      description: Input genomic vcf files
      pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bcf:
      type: file
      description: merged BCF file
      pattern: "*.bcf"
authors:
  - "@ramprasadn"