nf-core/amrfinderplus/run @ 0.0.0-0c7146d
Summary
Identify antimicrobial resistance in gene or protein sequences
Get started
Add the following snippet to your workflow script to include this module.
include { AMRFINDERPLUS_RUN } from 'nf-core/amrfinderplus/run'
License
MIT License
Name
|
AMRFINDERPLUS_RUN |
|---|
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}
|
db
file
|
A compressed tarball of the AMRFinderPlus database to query *.tar.gz
|
|---|
report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}.tsv
file
|
AMRFinder+ final report *.tsv
|
db_version
DBVER
string
|
The version of the used database in string format (useful for downstream tools such as hAMRronization) |
|---|
tool_version
VER
string
|
The version of the tool in string format (useful for downstream tools such as hAMRronization) |
|---|
mutation_report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}-mutations.tsv
file
|
Report of organism-specific point-mutations *-mutations.tsv
|
versions_amrfinderplus
tuple
${task.process}
string
|
Process name |
|---|---|
amrfinderplus
string
|
Tool name |
amrfinder --version
string
|
Tool version command |
versions_amrfinderplus_database
tuple
${task.process}
string
|
Process name |
|---|---|
amrfinderplus_database
string
|
Database name |
amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\.[0-9]+' | tail -1
string
|
Database version command |
| Tool | Description | Homepage |
|---|---|---|
| amrfinderplus | AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences. | https://github.com/ncbi/amr/wiki |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:21:55 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Famrfinderplus%2Frun/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/amrfinderplus/run/blobs/sha256:8a9621a5ad2190625d08bcecb1f5679c68df8769fb7667a4bbc3e6d38efdf517 |
| Size | 3.1 KB |
| Checksum | sha256:8a9621a5ad2190625d08bcecb1f5679c68df8769fb7667a4bbc3e6d38efdf517 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:21:55 (UTC) | 1 | 3.1 KB | - |