name: plink_vcf
description: Analyses variant calling files using plink
keywords:
  - plink
  - vcf
tools:
  - plink:
      description: |
        Whole genome association analysis toolset, designed to perform a range
        of basic, large-scale analyses in a computationally efficient manner
      homepage: "https://www.cog-genomics.org/plink"
      documentation: None
      tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev"
      doi: ""
      licence: ['GPL']

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

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"
  - bed:
      type: file
      description: PLINK binary biallelic genotype table
      pattern: "*.{bed}"
  - bim:
      type: file
      description: PLINK extended MAP file
      pattern: "*.{bim}"
  - fam:
      type: file
      description: PLINK sample information file
      pattern: "*.{fam}"

authors:
  - "@Mxrcon"
  - "@abhi18av"