name: gatk4_haplotypecaller
description: Call germline SNPs and indels via local re-assembly of haplotypes
keywords:
  - gatk4
  - haplotypecaller
  - haplotype
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"]

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"
  - 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"
  - dbsnp:
      type: file
      description: VCF file containing known sites (optional)
  - dbsnp_tbi:
      type: file
      description: VCF index of dbsnp (optional)

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: Index of VCF file
      pattern: "*.vcf.gz.tbi"
  - bam:
      type: file
      description: Assembled haplotypes and locally realigned reads
      pattern: "*.realigned.bam"

authors:
  - "@suzannejin"
  - "@FriederikeHanssen"
