name: nextclade_datasetget description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) keywords: - nextclade - variant - consensus tools: - nextclade: description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks homepage: https://github.com/nextstrain/nextclade documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade doi: "" licence: ['MIT'] input: - dataset: type: string description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command. pattern: ".+" - reference: type: string description: Accession id to download dataset based on a particular reference sequence. A list of available datasets can be obtained using the nextclade dataset list command. pattern: ".+" - tag: type: string description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command. pattern: ".+" output: - versions: type: file description: File containing software versions pattern: "versions.yml" - prefix: type: path description: A directory containing the dataset files needed for nextclade run pattern: "prefix" authors: - "@antunderwood" - "@drpatelh"