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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
64 lines
1.8 KiB
YAML
Executable file
64 lines
1.8 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_format:
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type: string
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description: |
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String for output format supported by nextclade
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i.e one of 'json', 'csv', 'tsv', 'tree', 'tsv-clades-only'
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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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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