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f20c427339
* added classic mlst module * removed nf-core TODO comments * included drpatelh suggestions * adjust version capture identation * update main to pass lint * follow output expected by test.yml * suggested prefix change from rpetit3 * Apply suggestions from code review Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
945 B
YAML
42 lines
945 B
YAML
name: mlst
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description: Run Torsten Seemann's classic MLST on a genome assembly
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keywords:
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- mlst
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tools:
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- mlst:
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description: Scan contig files against PubMLST typing schemes
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homepage: None
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documentation: None
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tool_dev_url: None
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doi: ""
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licence: ['GPL v2']
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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: Assembly fasta file
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pattern: "*.{fasta,fa,fna}"
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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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- tsv:
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type: file
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description: MLST calls in tsv format
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pattern: "*.{tsv}"
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authors:
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- "@lskatz"
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- "@tseemann"
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