Description

Identify antimicrobial resistance in gene or protein sequences

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

fasta:file

Nucleotide or protein sequences in FASTA format

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

db:file

A compressed tarball of the AMRFinderPlus database to query

*.tar.gz

Output

name:type
description
pattern

report

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}.tsv:file

AMRFinder+ final report

*.tsv

mutation_report

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}-mutations.tsv:file

Report of organism-specific point-mutations

*-mutations.tsv

versions

versions.yml:file

File containing software versions

versions.yml

tool_version

VER:string

The version of the tool in string format (useful for downstream tools such as hAMRronization)

db_version

DBVER:string

The version of the used database in string format (useful for downstream tools such as hAMRronization)

Tools

amrfinderplus
Public Domain

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.