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https://github.com/MillironX/nf-core_modules.git
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56 lines
1.5 KiB
YAML
56 lines
1.5 KiB
YAML
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name: sistr
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description: Serovar prediction of salmonella assemblies
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keywords:
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- bacteria
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- fasta
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- salmonella
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tools:
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- sistr:
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description: Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction
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homepage: https://github.com/phac-nml/sistr_cmd
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documentation: https://github.com/phac-nml/sistr_cmd
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tool_dev_url: https://github.com/phac-nml/sistr_cmd
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doi: "10.1371/journal.pone.0147101"
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licence: ['Apache-2.0']
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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: Nucleotide or protein sequences in FASTA format
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.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: SISTR serovar prediction
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pattern: "*.{tsv}"
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- allele_json:
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type: file
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description: Allele sequences and info to JSON
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pattern: "*.{json}"
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- allele_fasta:
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type: file
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description: FASTA file destination of novel cgMLST alleles
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pattern: "*.{fasta}"
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- cgmlst_csv:
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type: file
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description: CSV file destination for cgMLST allelic profiles
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pattern: "*.{csv}"
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authors:
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- "@rpetit3"
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