name: nextclade description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation) keywords: - nextclade - variant - consensus tools: - nextclade: description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation) homepage: https://clades.nextstrain.org documentation: None tool_dev_url: https://github.com/nextstrain/nextclade doi: "" licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: FASTA file containing one or more consensus sequences pattern: "*.{fasta,fa}" - output_format: type: string description: | String for output format supported by nextclade i.e one of 'json', 'csv', 'tsv', 'tree', 'tsv-clades-only' output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - csv: type: file description: CSV file containing nextclade results pattern: "*.{csv}" - json: type: file description: JSON file containing nextclade results pattern: "*.{json}" - json_tree: type: file description: Auspice JSON V2 containing nextclade results pattern: "*.{tree.json}" - tsv: type: file description: TSV file containing nextclade results pattern: "*.{tsv}" - tsv_clades: type: file description: TSV file containing nextclade results for clades only pattern: "*.{clades.tsv}" authors: - "@drpatelh"