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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
60 lines
1.7 KiB
YAML
60 lines
1.7 KiB
YAML
name: nextclade_run
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description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ 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
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homepage: https://github.com/nextstrain/nextclade
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documentation: https://github.com/nextstrain/nextclade
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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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- dataset:
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type: path
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description: Path containing the dataset files obtained by running nextclade dataset get
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pattern: "*"
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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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authors:
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- "@antunderwood"
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- "@drpatelh"
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