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Bactopia Tool - amrfinderplus

The amrfinderplus module uses AMRFinder+ to screen assemblies and proteins for antimicrobial resistance and virulence genes.

Example Usage

bactopia --wf amrfinderplus \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt  

Output Overview

Below is the default output structure for the amrfinderplus tool. Where possible the file descriptions below were modified from a tools description.

├── SRX4563671
│   ├── SRX4563671-genes.tsv
│   ├── SRX4563671-proteins.tsv
│   └── logs
│       └── amrfinderplus
│           ├── nf-amrfinderplus.{begin,err,log,out,run,sh,trace}
│           └── versions.yml
├── logs
│   ├── amrfinderplus
│   │   ├── nf-amrfinderplus.{begin,err,log,out,run,sh,trace}
│   │   └── versions.yml
│   ├── csvtk_concat
│   │   ├── nf-csvtk_concat.{begin,err,log,out,run,sh,trace}
│   │   └── versions.yml
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions.{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├──
│   ├── amrfinderplus-report.html
│   ├── amrfinderplus-timeline.html
│   └── amrfinderplus-trace.txt
├── amrfinderdb.tar.gz
├── amrfinderplus-genes.tsv
├── amrfinderplus-proteins.tsv
├── software_versions.yml
└── software_versions_mqc.yml


Top Level

Below are results that are in the base directory.

Filename Description
amrfinderdb.tar.gz A tarball of the AMRFinder+ database used during analysis
amrfinderplus-genes.tsv A merged TSV file with AMRFinder+ results using nucleotide inputs
amrfinderplus-proteins.tsv A merged TSV file with AMRFinder+ results using protein inputs


Below is a description of the per-sample results from AMRFinder+.

Extension Description
-genes.tsv A TSV file with AMRFinder+ results using nucleotide inputs
-proteins.tsv A TSV file with AMRFinder+ results using protein inputs

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.


Each process that is executed will have a logs folder containing helpful files for you to review if the need ever arises.

Filename Description
nf-<PROCESS_NAME>.begin An empty file used to designate the process started
nf-<PROCESS_NAME>.err Contains STDERR outputs from the process
nf-<PROCESS_NAME>.log Contains both STDERR and STDOUT outputs from the process
nf-<PROCESS_NAME>.out Contains STDOUT outputs from the process
nf-<PROCESS_NAME>.run The script Nextflow uses to stage/unstage files and queue processes based on given profile
nf-<PROCESS_NAME>.sh The script executed by bash for the process
nf-<PROCESS_NAME>.trace The Nextflow Trace report for the process
versions.yml A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename Description The Nextflow DAG visualisation
amrfinderplus-report.html The Nextflow Execution Report
amrfinderplus-timeline.html The Nextflow Timeline Report
amrfinderplus-trace.txt The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename Description
software_versions.yml A complete list of programs and versions used by each process
software_versions_mqc.yml A complete list of programs and versions formatted for MultiQC


Required Parameters

Define where the pipeline should find input data and save output data.

Parameter Description Default
--bactopia The path to bactopia results to use as inputs

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter Description Default
--include A text file containing sample names (one per line) to include from the analysis
--exclude A text file containing sample names (one per line) to exclude from the analysis

AMRFinder+ Parameters

Parameter Description Default
--amrfinder_db Path to your AMRFinder+ database as a tarball, if not given database will be built
--force_update Force AMRFinder+ to rebuild the database False
--ident_min Minimum proportion of identical amino acids in alignment for hit (0..1) -1
--coverage_min Minimum coverage of the reference protein (0..1) 0.5
--organism Taxonomy group to run additional screens against
--translation_table NCBI genetic code for translated BLAST 11
--report_common Report proteins common to a taxonomy group False
--report_all_equal Report all equally-scoring BLAST and HMM matches False
--amrfinder_opts Extra AMRFinder+ options in quotes.

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter Description Default
--outdir Base directory to write results to ./
--run_name Name of the directory to hold results bactopia
--skip_compression Ouput files will not be compressed False
--keep_all_files Keeps all analysis files created False

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter Description Default
--max_retry Maximum times to retry a process before allowing it to fail. 3
--max_cpus Maximum number of CPUs that can be requested for any single job. 4
--max_memory Maximum amount of memory (in GB) that can be requested for any single job. 32
--max_time Maximum amount of time (in minutes) that can be requested for any single job. 120
--max_downloads Maximum number of samples to download at a time 3

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter Description Default
--nfconfig A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_mode Method used to save pipeline results to output directory. copy
--infodir Directory to keep pipeline Nextflow logs and reports. ${params.outdir}/pipeline_info
--force Nextflow will overwrite existing output files. False
--cleanup_workdir After Bactopia is successfully executed, the work directory will be deleted. False

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter Description Default
--condadir Directory to Nextflow should use for Conda environments
--registry Docker registry to pull containers from. dockerhub
--singularity_cache Directory where remote Singularity images are stored.
--singularity_pull_docker_container Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuild Force overwrite of existing pre-built environments. False
--queue Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM) general,high-memory
--cluster_opts Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--disable_scratch All intermediate files created on worker nodes of will be transferred to the head node. False

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter Description Default
--monochrome_logs Do not use coloured log outputs.
--nfdir Print directory Nextflow has pulled Bactopia to
--sleep_time The amount of time (seconds) Nextflow will wait after setting up datasets before execution. 5
--validate_params Boolean whether to validate parameters against the schema at runtime True
--help Display help text.
--wf Specify which workflow or Bactopia Tool to execute bactopia
--list_wfs List the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_params Show all params when using --help
--help_all An alias for --help --show_hidden_params
--version Display version text.


If you use Bactopia and amrfinderplus in your analysis, please cite the following.