name: pangolin
description: Phylogenetic Assignment of Named Global Outbreak LINeages
keywords:
    - covid
    - pangolin
    - lineage
tools:
    - star:
        description: |
            Phylogenetic Assignment of Named Global Outbreak LINeages
        homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
        manual: https://github.com/cov-lineages/pangolin#pangolearn-description
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
    - fasta:
        type: file
        description: |
            The genome assembly to be evaluated
output:
    - report:
        type: file
        description: Pangolin lineage report
        pattern: "*.{csv}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@kevinmenden"
    - "@drpatelh"