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

Predict antibiotic resistance from protein or nucleotide data

bacteria fasta antibiotic resistance
Latest version: 0.0.0-6c4ed3a
Total downloads: 3
Source: nf-core/modules
Authors: @rpetit3 @jfy133 @jasmezz
Maintainers: @rpetit3 @jfy133 @jasmezz

Summary

Predict antibiotic resistance from protein or nucleotide data

Get started

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

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

License

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 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 08 Apr 2026 19:31:26 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Frgi%2Fmain/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/rgi/main/blobs/sha256:a17000fc287f8f0c72acc5ad638d7da1e7bdb0c6f5838e02c32b3c91b5ce1877
Size 3.8 KB
Checksum sha256:a17000fc287f8f0c72acc5ad638d7da1e7bdb0c6f5838e02c32b3c91b5ce1877
Downloads 1
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:40:46 (UTC) 1 3.8 KB
0.0.0-3fc6d40 22 Apr 2026 15:28:59 (UTC) 1 3.8 KB
0.0.0-0c7146d 08 Apr 2026 19:31:26 (UTC) 1