name: "gatk4_filtervarianttranches"
description: Apply tranche filtering
keywords:
  - filtervarianttranches
  - gatk4
  - tranche filtering
tools:
  - "gatk4":
      description: |
        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
        with a primary focus on variant discovery and genotyping. Its powerful processing engine
        and high-performance computing features make it capable of taking on projects of any size.
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]
      identifier: ""
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"
    - intervals:
        type: file
        description: Intervals
  - - 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:
  - vcf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz":
          type: file
          description: VCF file
          pattern: "*.vcf.gz"
  - tbi:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz.tbi":
          type: file
          description: VCF index file
          pattern: "*.vcf.gz.tbi"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@FriederikeHanssen"
maintainers:
  - "@FriederikeHanssen"
