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be798861c6
* add module for abricate * rename abricate/abricate to abricate/run * Update test.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
43 lines
1.2 KiB
YAML
43 lines
1.2 KiB
YAML
name: abricate_run
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description: Screen assemblies for antimicrobial resistance against multiple databases
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keywords:
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- bacteria
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- assembly
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- antimicrobial reistance
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tools:
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- abricate:
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description: Mass screening of contigs for antibiotic resistance genes
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homepage: https://github.com/tseemann/abricate
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documentation: https://github.com/tseemann/abricate
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tool_dev_url: https://github.com/tseemann/abricate
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doi: ""
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licence: ['GPL v2', '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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- assembly:
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type: file
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description: FASTA, GenBank or EMBL formatted file
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pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.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: Tab-delimited report of results
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pattern: "*.{txt}"
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authors:
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- "@rpetit3"
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