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6d6e3a018f
* add module for mykrobe predict and genotyphi parse * Update meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
51 lines
1.3 KiB
YAML
51 lines
1.3 KiB
YAML
name: "mykrobe_predict"
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description: AMR predictions for supported species
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keywords:
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- fastq
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- bam
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- antimicrobial resistance
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tools:
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- "mykrobe":
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description: "Antibiotic resistance prediction in minutes"
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homepage: "http://www.mykrobe.com/"
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documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
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tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
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doi: "10.1038/ncomms10063"
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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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- seqs:
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type: file
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description: BAM or FASTQ file
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pattern: "*.{bam,fastq.gz,fq.gz}"
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- species:
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type: string
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description: Species to make AMR prediction against
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pattern: "*"
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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: AMR predictions in CSV format
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pattern: "*.csv"
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- json:
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type: file
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description: AMR predictions in JSON format
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pattern: "*.json"
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authors:
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- "@rpetit3"
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