nf-core/hamronization/abricate @ 0.0.0-0c7146d
Summary
Tool to convert and summarize ABRicate outputs using the hAMRonization specification
Get started
Add the following snippet to your workflow script to include this module.
include { HAMRONIZATION_ABRICATE } from 'nf-core/hamronization/abricate'
License
MIT License
Process
Name
|
HAMRONIZATION_ABRICATE |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
report
file
|
Output TSV or CSV file from ABRicate *.{csv,tsv}
|
format
string
|
Type of report file to be produced tsv|json
|
|---|
software_version
string
|
Version of ABRicate used [0-9].[0-9].[0-9]
|
|---|
reference_db_version
string
|
Database version of ABRicate used [0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:46:34 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhamronization%2Fabricate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hamronization/abricate/blobs/sha256:13d58787d9f2940279b90a95196904f1971bee8ffbf00a6c13b6e53624fea5f1 |
| Size | 2.5 KB |
| Checksum | sha256:13d58787d9f2940279b90a95196904f1971bee8ffbf00a6c13b6e53624fea5f1 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:46:34 (UTC) | 1 | 2.5 KB | - |