name: nextclade_run description: 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: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - dataset: type: path description: Path containing the dataset files obtained by running nextclade dataset get pattern: "*" - fasta: type: file description: FASTA file containing one or more consensus sequences pattern: "*.{fasta,fa}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - 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}" authors: - "@antunderwood" - "@drpatelh"