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60 lines
1.6 KiB
YAML
60 lines
1.6 KiB
YAML
name: hicap
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description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
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keywords:
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- fasta
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- serotype
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- Haemophilus influenzae
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tools:
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- hicap:
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description: In silico typing of the H. influenzae capsule locus
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homepage: https://github.com/scwatts/hicap
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documentation: https://github.com/scwatts/hicap
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tool_dev_url: https://github.com/scwatts/hicap
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doi: "https://doi.org/10.1128/JCM.00190-19"
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licence: ["GPL v3"]
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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 formatted assembly file
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
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- database_dir:
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type: directory
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description: Optional - Directory containing locus database
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pattern: "*/*"
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- model_fp:
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type: file
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description: Optional - Prodigal model to use for gene prediction
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pattern: "*.{bin}"
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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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- gbk:
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type: file
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description: GenBank file and cap locus annotations
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pattern: "*.gbk"
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- svg:
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type: file
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description: Visualization of annotated cap locus
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pattern: "*.svg"
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- tsv:
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type: file
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description: Detailed summary of cap locus annotations
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pattern: "*.tsv"
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authors:
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- "@rpetit3"
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