name: tiddit_sv
description: Identify chromosomal rearrangements.
keywords:
    - structural
    - variants
    - vcf
tools:
    - sv:
        description:  Search for structural variants.
        homepage: https://github.com/SciLifeLab/TIDDIT
        documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
        doi: 10.12688/f1000research.11168.1
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:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Input FASTA file
        pattern: "*.{fasta,fa}"
    - fai:
        type: file
        description: FASTA index file
        pattern: "*.{fai}"
output:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - vcf:
        type: file
        description: vcf
        pattern: "*.{vcf}"
    - ploidy:
        type: file
        description: tab
        pattern: "*.{ploidy.tab}"
    - signals:
        type: file
        description: tab
        pattern: "*.{signals.tab}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@maxulysse"