nf-core/abritamr/run @ 0.0.0-0c7146d
A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes
| Tool | Description | Homepage |
|---|---|---|
| abritamr | A pipeline for running AMRfinderPlus and collating results into functional classes | https://github.com/MDU-PHL/abritamr |
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` |
|---|---|
fasta
file
|
Assembled contigs in FASTA format
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}
|
Output
6 channels
#1
out
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.amrfinder.out
string
|
raw output from AMRFinder plus (per sequence)
*.amrfinder.txt
|
#2
txt
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.abritamr.txt
string
|
Tab-delimited file, combining non-empty summary files
*.abritamr.txt
|
#3
matches
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.summary_matches.txt
file
|
Tab-delimited file, with a row per sequence, and columns representing functional drug classes
*.summary_matches.txt
|
#4
partials
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.summary_partials.txt
file
|
Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes
*.summary_partials.txt
|
#5
virulence
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.summary_virulence.txt
string
|
Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification
*.summary_virulence.txt
|
#6
versions_abritamr
tuple
${task.process}
string
|
The name of the process |
|---|---|
abritamr
string
|
The name of the tool |
abritamr --version 2>&1 | sed 's/^.*abritamr \([0-9.]*\).*/\1/'
eval
|
The expression to obtain the version of the tool |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 0c7146d85582628b5d1034504702fa808632b1af |
| Release Date | 08 Apr 2026 18:41:18 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fabritamr%2Frun/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/abritamr/run/blobs/sha256:3bb90639be1ca12c99b4fd6b051fa6e24cb5fb615309825a7668646b58eb202f |
| Size | 3.0 KB |
| Checksum | sha256:3bb90639be1ca12c99b4fd6b051fa6e24cb5fb615309825a7668646b58eb202f |
| Downloads | 6 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:18 (UTC) | PUBLISHED | 6 | 3.0 KB |