phaseimpute/modules/nf-core/beagle5/beagle/meta.yml at ad47858e9caca547760cd146597b212a4e388cf7 · gichas/phaseimpute · GitHub

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name: "beagle5_beagle"
description: Beagle v5.2 is a software package for phasing genotypes and for imputing
  ungenotyped markers.
keywords:
  - phasing
  - imputation
  - genotype
tools:
  - "beagle5":
      description: "Beagle is a software package for phasing genotypes and for imputing
        ungenotyped markers."
      homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html"
      documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf"
      doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015"
      licence: ["GPL v3"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - vcf:
        type: file
        description: target VCF input file to be imputed and or phased
        pattern: "*.{vcf,vcf.gz}"
  - - refpanel:
        type: file
        description: target reference panel
  - - genmap:
        type: file
        description: a PLINK format genetic map with cM units
        pattern: "*.{map,map.gz,map.zip}"
  - - exclsamples:
        type: file
        description: text file containing samples one sample per line to be excluded
          from the analysis
        pattern: "*.*"
  - - exclmarkers:
        type: file
        description: text file containing markers one marker per line to be excluded
          from the analysis
        pattern: "*.*"
output:
  - vcf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.vcf.gz":
          type: file
          description: bgzip compressed VCF file that contains phased non missing genotypes
            for all non reference samples
          pattern: "*.vcf.gz"
  - log:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.log":
          type: file
          description: a summary of the analysis that includes the Beagle version, the
            command line arguments, and compute time.
          pattern: "*.log"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@ashotmarg"
maintainers:
  - "@ashotmarg"