name: gatk4_calculatecontamination
description: |
  Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
keywords:
  - gatk4
  - calculatecontamination
  - cross-samplecontamination
  - getpileupsummaries
  - filtermutectcalls
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
      licence: ["Apache-2.0"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - pileup:
        type: file
        description: File containing the pileups summary table of a tumor sample to
          be used to calculate contamination.
        pattern: "*.pileups.table"
    - matched:
        type: file
        description: File containing the pileups summary table of a normal sample that
          matches with the tumor sample specified in pileup argument. This is an optional
          input.
        pattern: "*.pileups.table"
output:
  - contamination:
      - meta:
          type: file
          description: File containing the contamination table.
          pattern: "*.contamination.table"
      - "*.contamination.table":
          type: file
          description: File containing the contamination table.
          pattern: "*.contamination.table"
  - segmentation:
      - meta:
          type: file
          description: output table containing segmentation of tumor minor allele fractions
            (optional)
          pattern: "*.segmentation.table"
      - "*.segmentation.table":
          type: file
          description: output table containing segmentation of tumor minor allele fractions
            (optional)
          pattern: "*.segmentation.table"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@GCJMackenzie"
  - "@maxulysse"
maintainers:
  - "@GCJMackenzie"
  - "@maxulysse"
