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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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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