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48 lines
1.3 KiB
YAML
48 lines
1.3 KiB
YAML
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name: "seroba_run"
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description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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keywords:
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- fastq
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- serotype
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- Streptococcus pneumoniae
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tools:
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- "seroba":
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description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references."
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homepage: "https://sanger-pathogens.github.io/seroba/"
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documentation: "https://sanger-pathogens.github.io/seroba/"
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tool_dev_url: "https://github.com/sanger-pathogens/seroba"
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doi: "10.1099/mgen.0.000186"
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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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- reads:
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type: file
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description: Input Illunina paired-end FASTQ files
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pattern: "*.{fq.gz,fastq.gz}"
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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: The predicted serotype in tab-delimited format
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pattern: "*.tsv"
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- txt:
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type: file
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description: A detailed description of the predicted serotype
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pattern: "*.txt"
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authors:
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- "@rpetit3"
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