nf-core/abricate/run @ 0.0.0-0c7146d
Summary
Screen assemblies for antimicrobial resistance against multiple databases
Get started
Add the following snippet to your workflow script to include this module.
include { ABRICATE_RUN } from 'nf-core/abricate/run'
License
MIT License
Process
Name
|
ABRICATE_RUN |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
assembly
file
|
FASTA, GenBank or EMBL formatted file *.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}
|
databasedir
directory
|
Optional location of local copy of database files, possibly with custom databases set up with */
|
|---|
Output
2 channels
#1
report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Tab-delimited report of results *.{txt}
|
#2
versions_abricate
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
abricate
string
|
The tool name |
abricate --version | sed 's/^.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| abricate | Mass screening of contigs for antibiotic resistance genes | https://github.com/tseemann/abricate |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:20:51 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fabricate%2Frun/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/abricate/run/blobs/sha256:1c8c4e6014d5c3ac22a45f2c7e3f335399ac8477a5dda5e0a279f443a3116697 |
| Size | 2.5 KB |
| Checksum | sha256:1c8c4e6014d5c3ac22a45f2c7e3f335399ac8477a5dda5e0a279f443a3116697 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:20:51 (UTC) | 1 | 2.5 KB | - |