name: plink_extract
description: Subset plink bfiles with a text file of variant identifiers
keywords:
  - extract
  - plink
tools:
  - plink:
      description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
      homepage: None
      documentation: None
      tool_dev_url: None
      doi: ""
      licence: ["GPL"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - 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}"
  - variants:
      type: file
      description: A text file containing variant identifiers to keep (one per line)
      pattern: "*.{keep}"

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:
  - "@nebfield"