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:file

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

*.summary_matches.txt

${prefix}.summary_matches.txt:file

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

*.summary_matches.txt

partials

meta:file

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

*.summary_partials.txt

${prefix}.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:string

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

*.summary_virulence.txt

${prefix}.summary_virulence.txt:string

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

*.summary_virulence.txt

out

meta:string

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

${prefix}.amrfinder.out:string

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

txt

meta:string

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

${prefix}.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
maintainer
Github user rpetit3
get in touch
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