name: gatk4_filtermutectcalls
description: |
  Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
keywords:
  - filtermutectcalls
  - filter
  - gatk4
  - mutect2
  - vcf
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/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - vcf:
        type: file
        description: compressed vcf file of mutect2calls
        pattern: "*.vcf.gz"
    - vcf_tbi:
        type: file
        description: Tabix index of vcf file
        pattern: "*vcf.gz.tbi"
    - stats:
        type: file
        description: Stats file that pairs with output vcf file
        pattern: "*vcf.gz.stats"
    - orientationbias:
        type: file
        description: files containing artifact priors for input vcf. Optional input.
        pattern: "*.artifact-prior.tar.gz"
    - segmentation:
        type: file
        description: tables containing segmentation information for input vcf. Optional
          input.
        pattern: "*.segmentation.table"
    - table:
        type: file
        description: table(s) containing contamination data for input vcf. Optional
          input, takes priority over estimate.
        pattern: "*.contamination.table"
    - estimate:
        type: float
        description: estimation of contamination value as a double. Optional input,
          will only be used if table is not specified.
  - - meta2:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'genome' ]
    - fasta:
        type: file
        description: The reference fasta file
        pattern: "*.fasta"
  - - meta3:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'genome' ]
    - fai:
        type: file
        description: Index of reference fasta file
        pattern: "*.fasta.fai"
  - - meta4:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'genome' ]
    - dict:
        type: file
        description: GATK sequence dictionary
        pattern: "*.dict"
output:
  - vcf:
      - meta:
          type: file
          description: file containing filtered mutect2 calls.
          pattern: "*.vcf.gz"
      - "*.vcf.gz":
          type: file
          description: file containing filtered mutect2 calls.
          pattern: "*.vcf.gz"
  - tbi:
      - meta:
          type: file
          description: tbi file that pairs with vcf.
          pattern: "*.vcf.gz.tbi"
      - "*.vcf.gz.tbi":
          type: file
          description: tbi file that pairs with vcf.
          pattern: "*.vcf.gz.tbi"
  - stats:
      - meta:
          type: file
          description: file containing statistics of the filtermutectcalls run.
          pattern: "*.filteringStats.tsv"
      - "*.filteringStats.tsv":
          type: file
          description: file containing statistics of the filtermutectcalls run.
          pattern: "*.filteringStats.tsv"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@GCJMackenzie"
  - "@maxulysse"
  - "@ramprasadn"
maintainers:
  - "@GCJMackenzie"
  - "@maxulysse"
  - "@ramprasadn"
