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52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: amrfinderplus_run
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description: Identify antimicrobial resistance in gene or protein sequences
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keywords:
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- bacteria
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- fasta
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- antibiotic resistance
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tools:
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- amrfinderplus:
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description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
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homepage: https://github.com/ncbi/amr/wiki
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documentation: https://github.com/ncbi/amr/wiki
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tool_dev_url: https://github.com/ncbi/amr
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doi: "10.1038/s41598-021-91456-0"
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licence: ["Public Domain"]
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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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- db:
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type: file
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description: A compressed tarball of the AMRFinderPlus database to query
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pattern: "*.tar.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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- report:
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type: file
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description: AMRFinder+ final report
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pattern: "*.tsv"
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- mutation_report:
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type: file
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description: Report of organism-specific point-mutations
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pattern: "*-mutations.tsv"
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authors:
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- "@rpetit3"
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