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fc4f3e8822
* add seqsero2 module * correct lint errors * Update modules/seqsero2/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * set output directory Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: seqsero2
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description: Salmonella serotype prediction from reads and assemblies
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keywords:
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- fasta
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- fastq
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- salmonella
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- sertotype
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tools:
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- seqsero2:
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description: Salmonella serotype prediction from genome sequencing data
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homepage: https://github.com/denglab/SeqSero2
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documentation: https://github.com/denglab/SeqSero2
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tool_dev_url: https://github.com/denglab/SeqSero2
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doi: "10.1128/AEM.01746-19"
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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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- seqs:
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type: file
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description: FASTQ or FASTA formated sequences
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pattern: "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}"
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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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- log:
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type: file
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description: A log of serotype antigen results
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pattern: "*_log.txt"
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- tsv:
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type: file
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description: Tab-delimited summary of the SeqSero2 results
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pattern: "*_result.tsv"
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- txt:
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type: file
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description: Detailed summary of the SeqSero2 results
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pattern: "*_result.txt"
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authors:
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- "@rpetit3"
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