Nextflow Registry | nf-core/abritamr/run@0.0.0-0c7146d

nf-core/abritamr/run @ 0.0.0-0c7146d

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

bacteria fasta antibiotic resistance

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @rpetit3

Maintainers: @rpetit3 @sateeshperi

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

Add the following snippet to your workflow script to include this module.

include { ABRITAMR_RUN } from 'nf-core/abritamr/run'

MIT License

Process

`Name`	`ABRITAMR_RUN`

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

Tool	Description	Homepage
abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	https://github.com/MDU-PHL/abritamr

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:20:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fabritamr%2Frun/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/abritamr/run/blobs/sha256:bccb5189fe6851ffd878b403b5954ac3b7063ad99b98a33ef739bdfe2b49a544
Size	3.0 KB
Checksum	sha256:bccb5189fe6851ffd878b403b5954ac3b7063ad99b98a33ef739bdfe2b49a544
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:20:55 (UTC)		1	3.0 KB	-