abritamr_run

Tags: bacteria assembly fasta antimicrobial-resistance nata amrfinderplus sample-scope

Detect antimicrobial resistance and virulence genes.

Uses abriTAMR, a NATA (National Association of Testing Authorities) accredited pipeline, to report the presence of reportable AMR genes. It acts as a wrapper for AMRFinderPlus, formatted for clinical reporting standards used in Victoria, Australia.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    summary: Path?,
    matches: Path,
    partials: Path,
    virulence: Path,
    amrfinder: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
summary	Path?	Tab-delimited NATA-accredited AMR report summary
matches	Path	Tab-delimited list of matched AMR genes
partials	Path	Tab-delimited list of partially matched AMR genes
virulence	Path	Tab-delimited list of detected virulence genes
amrfinder	Path	Raw AMRFinderPlus output
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

abriTAMR Parameters

Parameter	Type	Default	Description
--abritamr_species	string		Use species specific point mutations, must provide a valid species
--abritamr_identity	integer		Minimum identity of matches with amrfinder (0 - 1.0), defaults to amrfinder preset

Used By

Subworkflows

• abritamr - Identify antimicrobial resistance genes using AMRFinderPlus.

Workflows

• abritamr - A NATA accredited tool for reporting the presence of antimicrobial resistance genes.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• abriTAMR
  Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, and Seemann T An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nature Communications, 14(1), 60. (2023)

Source

View source on GitHub

Version

ABRITAMR_RUN:
    - abritamr: 1.2.0