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.

amrfinderplus/
├── 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-dag.dot
│   ├── 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

Results¶

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

AMRFinder+¶

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.

Logs¶

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
amrfinderplus-dag.dot	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

Parameters¶

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¶