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: The lineage report
      pattern: "{prefix}.lineage_report.csv"

  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

authors:
  - "@kevinmenden"