name: "gvcftools_extractvariants"
description: Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.
keywords:
  - gvcftools
  - extract_variants
  - extractvariants
  - gvcf
  - vcf
tools:
  - "gvcftools":
      description: "gvcftools is a package of small utilities for creating and analyzing gVCF files"
      homepage: "{https://sites.google.com/site/gvcftools/home}"
      documentation: "{https://sites.google.com/site/gvcftools/home/configuration-and-analysis}"
      tool_dev_url: "{https://github.com/sequencing/gvcftools}"
      doi: ""
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gvcf:
      type: file
      description: GVCF file
      pattern: "*.{g.vcf,gvcf}.gz"

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"
  - vcf:
      type: file
      description: Converted variant-only VCF file
      pattern: "*.vcf.gz"

authors:
  - "@nvnieuwk"