name: gatk_createsequencedictionary
description: Creates a sequence dictionary for a reference sequence
keywords:
    - dictionary
    - fasta
tools:
    - gatk:
        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
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
input:
    - fasta:
        type: file
        description: Input fasta file
        pattern: "*.{fasta,fa}"
output:
    - bam:
        type: file
        description: gatk dictionary file
        pattern: "*.{dict}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@maxulysse"