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stxtyper

Tags: stx shiga-toxin typing stec virulence bactopia-tool

Identify and type Stx operons from assembled genomic sequences

This Bactopia Tool uses StxTyper to identify and type stx operons from assembled genomic sequences.

Usage​

Bactopia CLI:

bactopia --wf stxtyper \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/stxtyper/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs​

Expected Output Files​

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── stxtyper-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── stxtyper-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── stxtyper-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── stxtyper.tsv
        └── nf-reports
            ├── stxtyper-dag.dot
            ├── stxtyper-report.html
            └── stxtyper-timeline.html

Per-Sample Results​

FileDescription
*.tsvTab-delimited Stx operon typing results

Merged Results​

FileDescription
stxtyper.tsvMerged TSV file containing stxtyper results from all samples

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.

ExtensionDescription
.beginAn empty file used to designate the process started
.errContains STDERR outputs from the process
.logContains both STDERR and STDOUT outputs from the process
.outContains STDOUT outputs from the process
.runThe script Nextflow uses to stage/unstage files and queue processes based on given profile
.shThe script executed by bash for the process
.traceThe Nextflow trace report for the process
versions.ymlA 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.

FilenameDescription
stxtyper-dag.dotThe Nextflow DAG visualization
stxtyper-report.htmlThe Nextflow Execution Report
stxtyper-timeline.htmlThe Nextflow Timeline Report
stxtyper-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

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

ParameterTypeDefaultDescription
--bactopiastring-The path to bactopia results to use as inputs

csvtk concat Parameters​

ParameterTypeDefaultDescription
--csvtk_concat_optsstring-Extra csvtk concat options in quotes
Filtering Parameters

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

ParameterTypeDefaultDescription
--includestring-A text file containing sample names (one per line) to include from the analysis
--excludestring-A text file containing sample names (one per line) to exclude from the analysis
Optional Parameters

These optional parameters can be useful in certain settings.

ParameterTypeDefaultDescription
--outdirstringbactopiaBase directory to write results to
--skip_compressionbooleanfalseOutput files will not be compressed
--datasetsstring-The path to cache datasets to
--keep_all_filesbooleanfalseKeeps all analysis files created
Max Job Request Parameters

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

ParameterTypeDefaultDescription
--max_retryinteger3Maximum times to retry a process before allowing it to fail.
--max_cpusinteger4Maximum number of CPUs that can be requested for any single job.
--max_memorystring128.GBMaximum amount of memory that can be requested for any single job.
--max_timestring240.hMaximum amount of time that can be requested for any single job.
--max_downloadsinteger3Maximum number of samples to download at a time
Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--nfconfigstring-A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_modestringcopyMethod used to save pipeline results to output directory. (choices: symlink, rellink, link, copy, copyNoFollow, move)
--infodirstring${params.outdir}/pipeline_infoDirectory to keep pipeline Nextflow logs and reports.
--forcebooleanfalseNextflow will overwrite existing output files.
--cleanup_workdirbooleanfalseAfter Bactopia is successfully executed, the work directory will be deleted.
Institutional config options

Parameters used to describe centralized config profiles. These should not be edited.

ParameterTypeDefaultDescription
--custom_config_versionstringmasterGit commit id for Institutional configs.
--custom_config_basestringhttps://raw.githubusercontent.com/nf-core/configs/masterBase directory for Institutional configs.
--config_profile_namestring-Institutional config name.
--config_profile_descriptionstring-Institutional config description.
--config_profile_contactstring-Institutional config contact information.
--config_profile_urlstring-Institutional config URL link.
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--condadirstring-Directory to Nextflow should use for Conda environments
--registrystringquay.ioRegistry to pull Docker containers from.
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
--singularity_cachestring-Directory where remote Singularity images are stored.
--singularity_pull_docker_containerboolean-Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuildbooleanfalseForce overwrite of existing pre-built environments.
--queuestringgeneral,high-memoryComma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)
--cluster_optsstringAdditional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--container_optsstringAdditional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D pwd'
--disable_scratchbooleanfalseAll intermediate files created on worker nodes of will be transferred to the head node.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--monochrome_logsboolean-Do not use coloured log outputs.
--nfdirboolean-Print directory Nextflow has pulled Bactopia to
--sleep_timeinteger5The amount of time (seconds) Nextflow will wait after setting up datasets before execution.
--helpboolean-Display help text.
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsboolean-List the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_paramsboolean-Show all params when using --help
--help_allboolean-An alias for --help --show_hidden_params
--versionboolean-Display version text.

Composition​

This workflow uses the following subworkflows:

  • stxtyper - Identify and type Stx operons from assembled genomic sequences

Citations​

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

Source​

View source on GitHub