modules/abritamr_run

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

bacteriafastaantibiotic resistance

https://github.com/nf-core/modules/[...]/modules/nf-core/abritamr/run

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`matches`

`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

`partials`

`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

`virulence`

`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

`out`

`meta`
`:map`

Groovy Map containing sample information

`*.amrfinder.out`
`:string`

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

`txt`

`meta`
`:map`

Groovy Map containing sample information

`*.abritamr.txt`
`:string`

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

abritamr
GPL v3

A pipeline for running AMRfinderPlus and collating results into functional classes

github.com/MDU-PHL/abritamr 10.1038/s41467-022-35713-4