nf-core/hamronization/rgi @ 0.0.0-3fc6d40
Summary
Tool to convert and summarize RGI outputs using the hAMRonization specification.
Get started
Add the following snippet to your workflow script to include this module.
include { HAMRONIZATION_RGI } from 'nf-core/hamronization/rgi'
License
MIT License
Process
Name
|
HAMRONIZATION_RGI |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
report
file
|
Output .txt file from RGI *.txt
|
format
string
|
Type of report file to be produced tsv|json
|
|---|
software_version
string
|
Version of DeepARG used [0-9].[0-9].[0-9]
|
|---|
reference_db_version
string
|
Database version of DeepARG used [0-9].[0-9].[0-9]
|
|---|
Output
3 channels
#1
tsv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tsv
file
|
hAMRonised report in TSV format *.json
|
#2
json
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.json
file
|
hAMRonised report in JSON format *.json
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| hamronization | Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification | https://github.com/pha4ge/hAMRonization/ |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:15:55 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fhamronization%2Frgi/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hamronization/rgi/blobs/sha256:293710b4b57426ff78859687ff32fbba678890a436ee20749bc4a7c742673e35 |
| Size | 2.7 KB |
| Checksum | sha256:293710b4b57426ff78859687ff32fbba678890a436ee20749bc4a7c742673e35 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:23:24 (UTC) | 4 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:15:55 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:08:30 (UTC) | 3 | 2.7 KB |