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/` - 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"