name: gatk4_calibratedragstrmodel
description: estimates the parameters for the DRAGstr model
keywords:
  - gatk4
  - bam
  - cram
  - sam
  - calibratedragstrmodel
tools:
  - gatk4:
      description:
        Genome Analysis Toolkit (GATK4). 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/articles/360057441571-CalibrateDragstrModel-BETA-
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]

input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - bam_index:
      type: file
      description: index of the BAM/CRAM/SAM file
      pattern: "*.{bai,crai,sai}"
  - intervals:
      type: file
      description: BED file or interval list containing regions (optional)
      pattern: "*.{bed,interval_list}"
  - fasta:
      type: file
      description: The reference FASTA file
      pattern: "*.{fasta,fa}"
  - fasta_fai:
      type: file
      description: The index of the reference FASTA file
      pattern: "*.fai"
  - dict:
      type: file
      description: The sequence dictionary of the reference FASTA file
      pattern: "*.dict"
  - strtablefile:
      type: file
      description: The StrTableFile zip folder of the reference FASTA file
      pattern: "*.zip"

output:
  #Only when we have meta
  - 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"
  - dragstr_model:
      type: file
      description: The DragSTR model
      pattern: "*.txt"

authors:
  - "@nvnieuwk"