name: snpsift_split
description: Splits/Joins VCF(s) file into chromosomes
keywords:
  - split
  - join
  - vcf
tools:
  - snpsift:
      description: SnpSift is a toolbox that allows you to filter and manipulate annotated files
      homepage: https://pcingola.github.io/SnpEff/ss_introduction/
      documentation: https://pcingola.github.io/SnpEff/ss_introduction/
      tool_dev_url: https://github.com/pcingola/SnpEff
      doi: "10.3389/fgene.2012.00035"
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file (split) or list of files (join)
      description: VCF file(s)
      pattern: "*.{vcf,vcf.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"
  - out_vcfs:
      type: file
      description: Split/Joined VCF file(s)
      pattern: "*.vcf"

authors:
  - "@SusiJo"
  - "@jonasscheid"
