name: gatk4_haplotypecaller
description: Call germline SNPs and indels via local re-assembly of haplotypes
keywords:
  - gatk4
  - haplotype
  - haplotypecaller
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', single_end:false ]
    - input:
        type: file
        description: BAM/CRAM file from alignment
        pattern: "*.{bam,cram}"
    - input_index:
        type: file
        description: BAI/CRAI file from alignment
        pattern: "*.{bai,crai}"
    - intervals:
        type: file
        description: Bed file with the genomic regions included in the library (optional)
    - dragstr_model:
        type: file
        description: Text file containing the DragSTR model of the used BAM/CRAM file
          (optional)
        pattern: "*.txt"
  - - meta2:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'test_reference' ]
    - fasta:
        type: file
        description: The reference fasta file
        pattern: "*.fasta"
  - - meta3:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'test_reference' ]
    - fai:
        type: file
        description: Index of reference fasta file
        pattern: "fasta.fai"
  - - meta4:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'test_reference' ]
    - dict:
        type: file
        description: GATK sequence dictionary
        pattern: "*.dict"
  - - meta5:
        type: map
        description: |
          Groovy Map containing dbsnp information
          e.g. [ id:'test_dbsnp' ]
    - dbsnp:
        type: file
        description: VCF file containing known sites (optional)
  - - meta6:
        type: map
        description: |
          Groovy Map containing dbsnp information
          e.g. [ id:'test_dbsnp' ]
    - dbsnp_tbi:
        type: file
        description: VCF index of dbsnp (optional)
output:
  - vcf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz":
          type: file
          description: Compressed VCF file
          pattern: "*.vcf.gz"
  - tbi:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.tbi":
          type: file
          description: Index of VCF file
          pattern: "*.vcf.gz.tbi"
  - bam:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.realigned.bam":
          type: file
          description: Assembled haplotypes and locally realigned reads
          pattern: "*.realigned.bam"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@suzannejin"
  - "@FriederikeHanssen"
maintainers:
  - "@suzannejin"
  - "@FriederikeHanssen"
