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"