mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
f91abed951
* Export versions as explicit emission strings in addition to versions.yml for compatibility with hAMRonization * Update YML
53 lines
2 KiB
YAML
53 lines
2 KiB
YAML
name: rgi_main
|
|
description: Predict antibiotic resistance from protein or nucleotide data
|
|
keywords:
|
|
- bacteria
|
|
- fasta
|
|
- antibiotic resistance
|
|
tools:
|
|
- rgi:
|
|
description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
|
|
homepage: https://card.mcmaster.ca
|
|
documentation: https://github.com/arpcard/rgi
|
|
tool_dev_url: https://github.com/arpcard/rgi
|
|
doi: "10.1093/nar/gkz935"
|
|
licence: ["https://card.mcmaster.ca/about"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: Nucleotide or protein sequences in FASTA format
|
|
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- json:
|
|
type: file
|
|
description: JSON formatted file with RGI results
|
|
pattern: "*.{json}"
|
|
- tsv:
|
|
type: file
|
|
description: Tab-delimited file with RGI results
|
|
pattern: "*.{txt}"
|
|
- tool_version:
|
|
type: string
|
|
description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
|
|
- db_version:
|
|
type: string
|
|
description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
|
|
authors:
|
|
- "@rpetit3"
|
|
- "@jfy133"
|