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