name: gatk4_fastqtosam
description: Converts FastQ file to BAM format
keywords:
  - bam
  - fastq
  - convert
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/categories/360002369672s
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: "10.1158/1538-7445.AM2017-3590"
      licence: ['BSD-3-clause']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,
              respectively.
      pattern: "*.fastq.gz"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - bam:
      type: file
      description: Converted BAM file
      pattern: "*.bam"

authors:
  - "@ntoda03"