Nextflow Registry | nf-core/rgi/main@0.0.0-0c7146d

nf-core/rgi/main @ 0.0.0-0c7146d

Predict antibiotic resistance from protein or nucleotide data

bacteria fasta antibiotic resistance

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @rpetit3 @jfy133 @jasmezz

Maintainers: @rpetit3 @jfy133 @jasmezz

Predict antibiotic resistance from protein or nucleotide data

Add the following snippet to your workflow script to include this module.

include { RGI_MAIN } from 'nf-core/rgi/main'

MIT License

Process

`Name`	`RGI_MAIN`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Nucleotide or protein sequences in FASTA format `*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}`

`card` directory	Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). `*/`

`wildcard` directory	Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). `*/`

Output 6 channels

#1 tmp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`temp/` directory	Directory containing various intermediate files `temp/`

#2 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt` file	Tab-delimited file with RGI results `*.{txt}`

#3 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json` file	JSON formatted file with RGI results `*.{json}`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 db_version

`DB_VERSION` string	The version of the used database in string format (useful for downstream tools such as hAMRronization)

#6 tool_version

`RGI_VERSION` string	The version of the tool in string format (useful for downstream tools such as hAMRronization)

Tool	Description	Homepage
rgi	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	https://card.mcmaster.ca

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:07:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Frgi%2Fmain/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/rgi/main/blobs/sha256:356045307cda9197a25ceb07a657912e5bfe3f358e0c05b6e3a4cf1270d85080
Size	3.8 KB
Checksum	sha256:356045307cda9197a25ceb07a657912e5bfe3f358e0c05b6e3a4cf1270d85080
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:07:55 (UTC)		1	3.8 KB	-