name: gatk4_getpileupsummaries
description: |
  Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
keywords:
  - gatk4
  - germlinevariantsites
  - getpileupsumaries
  - readcountssummary
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' ]
    - input:
        type: file
        description: BAM/CRAM file to be summarised.
        pattern: "*.{bam,cram}"
    - index:
        type: file
        description: Index file for the input BAM/CRAM file.
        pattern: "*.{bam.bai,cram.crai}"
    - intervals:
        type: file
        description: File containing specified sites to be used for the summary. If
          this option is not specified, variants file is used instead automatically.
        pattern: "*.interval_list"
  - - 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"
  - - variants:
        type: file
        description: Population vcf of germline sequencing, containing allele fractions.
          Is also used as sites file if no separate sites file is specified.
        pattern: "*.vcf.gz"
  - - variants_tbi:
        type: file
        description: Index file for the germline resource.
        pattern: "*.vcf.gz.tbi"
output:
  - table:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.pileups.table":
          type: file
          description: Table containing read counts for each site.
          pattern: "*.pileups.table"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@GCJMackenzie"
maintainers:
  - "@GCJMackenzie"
