... | ... | @@ -6,7 +6,7 @@ To run PathoFact you need to adjust some parameters in `config.yaml`. |
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- `project`: A unique project name which will be used as the name of the output directory in `datapath` path (see below).
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- `datapath`: Path to directory containing the sample data; the output directory will be created there.
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- `workflow`: Pathofact can run the complete pipeline (default) or a specific step:
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- "complete": complete pipeline = toxin + virulence + AMR + MGE prediction
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- "**complete**": *toxin* + *virulence* + *AMR* + *MGE* prediction
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- "Tox": toxin prediction
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- "Vir": virulence prediction
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- "AMR": antimicrobial resistance (AMR) & mobile genetic elements (MGEs) prediction
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