name: "gatk4_composestrtablefile"
description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
keywords:
  - gatk4
  - composestrtablefile
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/4405451249819-ComposeSTRTableFile
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]

input:
  - fasta:
      type: file
      description: FASTA reference file
      pattern: "*.{fasta,fa}"
  - fasta_fai:
      type: file
      description: index of the FASTA reference file
      pattern: "*.fai"
  - dict:
      type: file
      description: Sequence dictionary of the FASTA reference file
      pattern: "*.dict"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - str_table:
      type: file
      description: A zipped folder containing the STR table files
      pattern: "*.zip"

authors:
  - "@nvnieuwk"