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"