name: "gatk4_filtervarianttranches"
description: Apply tranche filtering
keywords:
  - gatk4
  - filtervarianttranches

tools:
  - "gatk4":
      description: Genome Analysis Toolkit (GATK4)
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: "10.1158/1538-7445.AM2017-3590"
      licence: ["BSD-3-clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: a VCF file containing variants, must have info key:CNN_2D
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: tbi file matching with -vcf
      pattern: "*.vcf.gz.tbi"
  - resources:
      type: list
      description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
      pattern: "*.vcf.gz"
  - resources_index:
      type: list
      description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
      pattern: "*.vcf.gz"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: Index of reference fasta file
      pattern: "fasta.fai"
  - dict:
      type: file
      description: GATK sequence dictionary
      pattern: ".dict"

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: VCF file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: VCF index file
      pattern: "*.vcf.gz.tbi"

authors:
  - "@FriederikeHanssen"
