nf-core_modules/modules/nextclade/meta.yml

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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:
- 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: "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}"
- tsv_clades:
type: file
description: TSV file containing nextclade results for clades only
pattern: "*.{clades.tsv}"
authors:
- "@drpatelh"