Description

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

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

fasta{:bash}

:file

Assembled contigs in FASTA format

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}

Output

name:type
description
pattern

matches{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.summary_matches.txt{:bash}

:file

Tab-delimited file, with a row per sequence, and columns representing functional drug classes

*.summary_matches.txt

partials{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.summary_partials.txt{:bash}

:file

Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes

*.summary_partials.txt

virulence{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.summary_virulence.txt{:bash}

:string

Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification

*.summary_virulence.txt

out{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.amrfinder.out{:bash}

:string

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

txt{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.abritamr.txt{:bash}

:string

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

versions_abritamr{:bash}

${task.process}{:bash}

:string

The name of the process

abritamr{:bash}

:string

The name of the tool

abritamr --version 2>&1 | sed 's/^.*abritamr \([0-9.]*\).*/\1/'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

abritamr{:bash}

:string

The name of the tool

abritamr --version 2>&1 | sed 's/^.*abritamr \([0-9.]*\).*/\1/'{:bash}

:eval

The expression to obtain the version of the tool

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
maintainers
Github user rpetit3
Github user sateeshperi
get in touch
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