Bactopia Tool - `staphtyper`¶

The staphtyper subworkflow includes multiple tools that are specific for typing certain features of Staphylococcus aureus. Currently staphtyper includes

AgrVATE - agr locus type and agr operon variants.
spaTyper - spa type
staphopia-sccmec - SCCmec type

This tool will evolve with S. aureus genomics, so you can expect it to add more typing methods (maybe even replace current methods) in the future. If a certain typing method for S. aureus please feel free to suggest it be added!~

Example Usage¶

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

Output Overview¶

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

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       ├── agrvate
│       │   ├── <SAMPLE_NAME>-agr_gp.tab
│       │   ├── <SAMPLE_NAME>-blastn_log.txt
│       │   ├── <SAMPLE_NAME>-summary.tab
│       │   └── logs
│       │       ├── nf-agrvate.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       ├── spatyper
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf-spatyper.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── staphopiasccmec
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf-staphopiasccmec.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── staphtyper-<TIMESTAMP>
        ├── merged-results
        │   ├── agrvate.tsv
        │   ├── logs
        │   │   ├── agrvate-concat
        │   │   │   ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── spatyper-concat
        │   │   │   ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   └── staphopiasccmec-concat
        │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   ├── spatyper.tsv
        │   └── staphopiasccmec.tsv
        └── nf-reports
            ├── staphtyper-dag.dot
            ├── staphtyper-report.html
            ├── staphtyper-timeline.html
            └── staphtyper-trace.txt

Directory structure might be different

staphtyper is available as a standalone Bactopia Tool, as well as from the main Bactopia workflow (e.g. through Staphopia or Merlin). If executed from Bactopia, the staphtyper directory structure might be different, but the output descriptions below still apply.

Results¶

Merged Results¶

Below are results that are concatenated into a single file.

Filename	Description
agrvate.tsv	A merged TSV file with `AgrVATE` results from all samples
spatyper.tsv	A merged TSV file with `spaTyper` results from all samples
staphopiasccmec.tsv	A merged TSV file with `staphopia-sccmec` results from all samples

AgrVATE¶

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

Extension	Description
-agr_gp.tab	A detailed report for agr kmer matches
-blastn_log.txt	Log files from programs called by `AgrVATE`
-summary.tab	A final summary report for agr typing

spaTyper¶

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

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with `spaTyper` result

staphopia-sccmec¶

Below is a description of the per-sample results from staphopia-sccmec.

Filename	Description
<SAMPLE_NAME>.tsv	A tab-delimited file with `staphopia-sccmec` results

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 folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.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
staphtyper-dag.dot	The Nextflow DAG visualisation
staphtyper-report.html	The Nextflow Execution Report
staphtyper-timeline.html	The Nextflow Timeline Report
staphtyper-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
`--bactopia`	The path to bactopia results to use as inputs Type: `string`

Filtering Parameters¶

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

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

AgrVATE Parameters¶

Parameter	Description
`--typing_only`	agr typing only. Skips agr operon extraction and frameshift detection Type: `boolean`

spaTyper Parameters¶

Parameter	Description
`--repeats`	List of spa repeats Type: `string`
`--repeat_order`	List spa types and order of repeats Type: `string`
`--do_enrich`	Do PCR product enrichment Type: `boolean`

staphopia-sccmec Parameters¶

Parameter	Description
`--hamming`	Report the results as hamming distances Type: `boolean`

Optional Parameters¶

These optional parameters can be useful in certain settings.

Parameter	Description
`--outdir`	Base directory to write results to Type: `string`, Default: `./`
`--run_name`	Name of the directory to hold results Type: `string`, Default: `bactopia`
`--skip_compression`	Ouput files will not be compressed Type: `boolean`
`--datasets`	The path to cache datasets to Type: `string`
`--keep_all_files`	Keeps all analysis files created Type: `boolean`

Max Job Request Parameters¶

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

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

Nextflow Configuration Parameters¶

Parameters to fine-tune your Nextflow setup.

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

Nextflow Profile Parameters¶