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‎docs/bactopia-tools/clermontyping.md

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---
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title: clermontyping
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description: A Bactopia Tool which uses ClermonTyping to conduct _in silico_ phylotyping of _Escherichia_ genomes.
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---
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# Bactopia Tool - `clermontyping`
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The `clermontyping` module used [ClermonTyping](https://github.com/happykhan/ClermonTyping)
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to conduct _in silico_ prediction of phylotype for _Escherichia_ genomes. It uses the
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genome assemblies to be assign them to _E. albertii_, _E. fergusonii_, _Escherichia_
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clades I–V, _E. coli sensu stricto_ as well as to the main _E. coli_ phylogroups
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## Example Usage
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```
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bactopia --wf clermontyping \
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--bactopia /path/to/your/bactopia/results
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```
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## Output Overview
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Below is the default output structure for the `clermontyping` tool. Where possible the
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file descriptions below were modified from a tools description.
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```{bash}
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<BACTOPIA_DIR>
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├── <SAMPLE_NAME>
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│ └── tools
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│ └── clermontyping
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│ ├── <SAMPLE_NAME>.blast.xml
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│ ├── <SAMPLE_NAME>.html
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│ ├── <SAMPLE_NAME>.mash.tsv
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│ ├── <SAMPLE_NAME>.phylogroups.txt
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│ └── logs
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│ ├── nf-clermontyping.{begin,err,log,out,run,sh,trace}
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│ └── versions.yml
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└── bactopia-runs
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└── clermontyping
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├── merged-results
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│ ├── clermontyping.tsv
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│ └── logs
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│ └── clermontyping-concat
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│ ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
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│ └── versions.yml
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└── nf-reports
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├── clermontyping-dag.dot
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├── clermontyping-report.html
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├── clermontyping-timeline.html
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└── clermontyping-trace.txt
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```
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!!! info "Directory structure might be different"
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`clermontyping` is available as a standalone Bactopia Tool, as well as from
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the main Bactopia workflow (e.g. through Staphopia or Merlin). If executed
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from Bactopia, the `clermontyping` directory structure might be different, but the
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output descriptions below still apply.
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### Results
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#### Merged Results
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Below are results that are concatenated into a single file.
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| Filename | Description |
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|-------------------------------|-------------|
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| clermontyping.csv | A merged TSV file with `ClermonTyping` results from all samples |
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#### ClermonTyping
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Below is a description of the _per-sample_ results from [ClermonTyping](https://github.com/happykhan/ClermonTyping).
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| Extension | Description |
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|-------------------------------|-------------|
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| &lt;SAMPLE_NAME&gt;.blast.xml | A BLAST XML file with the results of the ClermonTyping analysis |
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| &lt;SAMPLE_NAME&gt;.html | A HTML file with the results of the ClermonTyping analysis |
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| &lt;SAMPLE_NAME&gt;.mash.tsv | A TSV file with the Mash distances |
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| &lt;SAMPLE_NAME&gt;.phylogroups.txt | A TSV file with the final phylogroup assignments |
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### Audit Trail
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Below are files that can assist you in understanding which parameters and program versions were used.
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#### Logs
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Each process that is executed will have a folder named `logs`. In this folder are helpful
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files for you to review if the need ever arises.
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| Extension | Description |
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|--------------|-------------|
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| .begin | An empty file used to designate the process started |
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| .err | Contains STDERR outputs from the process |
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| .log | Contains both STDERR and STDOUT outputs from the process |
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| .out | Contains STDOUT outputs from the process |
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| .run | The script Nextflow uses to stage/unstage files and queue processes based on given profile |
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| .sh | The script executed by bash for the process |
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| .trace | The Nextflow [Trace](https://www.nextflow.io/docs/latest/tracing.html#trace-report) report for the process |
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| versions.yml | A YAML formatted file with program versions |
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#### Nextflow Reports
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These Nextflow reports provide great a great summary of your run. These can be used to optimize
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resource usage and estimate expected costs if using cloud platforms.
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| Filename | Description |
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|----------|-------------|
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| clermontyping-dag.dot | The Nextflow [DAG visualisation](https://www.nextflow.io/docs/latest/tracing.html#dag-visualisation) |
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| clermontyping-report.html | The Nextflow [Execution Report](https://www.nextflow.io/docs/latest/tracing.html#execution-report) |
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| clermontyping-timeline.html | The Nextflow [Timeline Report](https://www.nextflow.io/docs/latest/tracing.html#timeline-report) |
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| clermontyping-trace.txt | The Nextflow [Trace](https://www.nextflow.io/docs/latest/tracing.html#trace-report) report |
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#### Program Versions
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At the end of each run, each of the `versions.yml` files are merged into the files below.
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| Filename | Description |
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|---------------------------|-------------|
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| software_versions.yml | A complete list of programs and versions used by each process |
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| software_versions_mqc.yml | A complete list of programs and versions formatted for [MultiQC](https://multiqc.info/) |
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## Parameters
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### <i class="fa-xl fas fa-terminal"></i> Required Parameters
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Define where the pipeline should find input data and save output data.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-bacterium"></i>` --bactopia` | The path to bactopia results to use as inputs <br/>**Type:** `string` |
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### <i class="fa-xl fa-solid fa-filter"></i> Filtering Parameters
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Use these parameters to specify which samples to include or exclude.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg far fa-square-plus"></i>` --include` | A text file containing sample names (one per line) to include from the analysis <br/>**Type:** `string` |
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| <i class="fa-lg far fa-square-minus"></i>` --exclude` | A text file containing sample names (one per line) to exclude from the analysis <br/>**Type:** `string` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> ClermonTyping Parameters
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-file-alt"></i>` --clermon_threshold` | Do not use contigs under this size <br/>**Type:** `number` |
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### <i class="fa-xl fa-solid fa-gears"></i> Optional Parameters
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These optional parameters can be useful in certain settings.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-folder"></i>` --outdir` | Base directory to write results to <br/>**Type:** `string`, **Default:** `bactopia` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --skip_compression` | Ouput files will not be compressed <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-folder"></i>` --datasets` | The path to cache datasets to <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-trash-restore"></i>` --keep_all_files` | Keeps all analysis files created <br/>**Type:** `boolean` |
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### <i class="fa-xl fa-solid fa-arrow-up-right-dots"></i> Max Job Request Parameters
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Set the top limit for requested resources for any single job.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
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| <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
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| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
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| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
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| <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
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### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters
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Parameters to fine-tune your Nextflow setup.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-cog"></i>` --nfconfig` | A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set. <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-copy"></i>` --publish_dir_mode` | Method used to save pipeline results to output directory. <br/>**Type:** `string`, **Default:** `copy` |
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| <i class="fa-lg fas fa-cogs"></i>` --infodir` | Directory to keep pipeline Nextflow logs and reports. <br/>**Type:** `string`, **Default:** `${params.outdir}/pipeline_info` |
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| <i class="fa-lg fas fa-recycle"></i>` --force` | Nextflow will overwrite existing output files. <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-trash-alt"></i>` --cleanup_workdir` | After Bactopia is successfully executed, the `work` directory will be deleted. <br/>**Type:** `boolean` |
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### <i class="fa-xl fas fa-university"></i> Institutional config options
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Parameters used to describe centralized config profiles. These should not be edited.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-users-cog"></i>` --custom_config_version` | Git commit id for Institutional configs. <br/>**Type:** `string`, **Default:** `master` |
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| <i class="fa-lg fas fa-users-cog"></i>` --custom_config_base` | Base directory for Institutional configs. <br/>**Type:** `string`, **Default:** `https://raw.githubusercontent.com/nf-core/configs/master` |
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| <i class="fa-lg fas fa-users-cog"></i>` --config_profile_name` | Institutional config name. <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-users-cog"></i>` --config_profile_description` | Institutional config description. <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-users-cog"></i>` --config_profile_contact` | Institutional config contact information. <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-users-cog"></i>` --config_profile_url` | Institutional config URL link. <br/>**Type:** `string` |
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### <i class="fa-xl fa-regular fa-address-card"></i> Nextflow Profile Parameters
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Parameters to fine-tune your Nextflow setup.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-folder"></i>` --condadir` | Directory to Nextflow should use for Conda environments <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-box"></i>` --registry` | Docker registry to pull containers from. <br/>**Type:** `string`, **Default:** `dockerhub` |
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| <i class="fa-lg fas fa-folder"></i>` --datasets_cache` | Directory where downloaded datasets should be stored. <br/>**Type:** `string`, **Default:** `<BACTOPIA_DIR>/data/datasets` |
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| <i class="fa-lg fas fa-folder"></i>` --singularity_cache_dir` | Directory where remote Singularity images are stored. <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-toolbox"></i>` --singularity_pull_docker_container` | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-recycle"></i>` --force_rebuild` | Force overwrite of existing pre-built environments. <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-clipboard-list"></i>` --queue` | Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM) <br/>**Type:** `string`, **Default:** `general,high-memory` |
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| <i class="fa-lg fas fa-clipboard-list"></i>` --cluster_opts` | Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name' <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-clipboard-list"></i>` --container_opts` | Additional options to pass to Apptainer, Docker, or Singularityu. (e.g. Singularity: '-D `pwd`' <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-toggle-off"></i>` --disable_scratch` | All intermediate files created on worker nodes of will be transferred to the head node. <br/>**Type:** `boolean` |
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### <i class="fa-xl fa-solid fa-reply-all"></i> Helpful Parameters
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Uncommonly used parameters that might be useful.
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-palette"></i>` --monochrome_logs` | Do not use coloured log outputs. <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-remove-format"></i>` --nfdir` | Print directory Nextflow has pulled Bactopia to <br/>**Type:** `boolean` |
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| <i class="fa-lg far fa-clock"></i>` --sleep_time` | The amount of time (seconds) Nextflow will wait after setting up datasets before execution. <br/>**Type:** `integer`, **Default:** `5` |
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| <i class="fa-lg fas fa-tasks"></i>` --validate_params` | Boolean whether to validate parameters against the schema at runtime <br/>**Type:** `boolean`, **Default:** `True` |
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| <i class="fa-lg fas fa-question-circle"></i>` --help` | Display help text. <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-bacteria"></i>` --wf` | Specify which workflow or Bactopia Tool to execute <br/>**Type:** `string`, **Default:** `bactopia` |
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| <i class="fa-lg fas fa-list"></i>` --list_wfs` | List the available workflows and Bactopia Tools to use with '--wf' <br/>**Type:** `boolean` |
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| <i class="fa-lg far fa-eye"></i>` --show_hidden_params` | Show all params when using `--help` <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-question-circle"></i>` --help_all` | An alias for --help --show_hidden_params <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-info"></i>` --version` | Display version text. <br/>**Type:** `boolean` |
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## Citations
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If you use Bactopia and `clermontyping` in your analysis, please cite the following.
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- [Bactopia](https://bactopia.github.io/)
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Petit III RA, Read TD [Bactopia - a flexible pipeline for complete analysis of bacterial genomes.](https://doi.org/10.1128/mSystems.00190-20) _mSystems_ 5 (2020)
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- [ClermontTyping](https://github.com/happykhan/ClermonTyping)
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Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. [ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping.](https://doi.org/10.1099/mgen.0.000192) Microbial Genomics, 4(7), e000192. (2018)
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- [csvtk](https://bioinf.shenwei.me/csvtk/)
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Shen, W [csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang.](https://github.com/shenwei356/csvtk/) (GitHub)
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‎docs/bactopia-tools/merlin.md

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| <i class="fa-lg fa-solid fa-toggle-on"></i>` --typing_only` | agr typing only. Skips agr operon extraction and frameshift detection <br/>**Type:** `boolean` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> ClermonTyping Parameters
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-file-alt"></i>` --clermon_threshold` | Do not use contigs under this size <br/>**Type:** `number` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> ECTyper Parameters
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --hamming` | Report the results as hamming distances <br/>**Type:** `boolean` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> TBProfiler Profile Parameters
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --call_whole_genome` | Call whole genome <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --mapper` | Mapping tool to use. If you are using nanopore data it will default to minimap2 <br/>**Type:** `string`, **Default:** `bwa` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --caller` | Variant calling tool to use <br/>**Type:** `string`, **Default:** `freebayes` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --calling_params` | Extra variant caller options in quotes <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --suspect` | Use the suspect suite of tools to add ML predictions <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_flagstat` | Don't collect flagstats <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_delly` | Don't run delly <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-italic"></i>` --tbprofiler_opts` | Extra options in quotes for TBProfiler <br/>**Type:** `string` |
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### <i class="fa-xl fa-solid fa-gears"></i> Optional Parameters
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These optional parameters can be useful in certain settings.

‎docs/bactopia-tools/tbprofiler.md

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| <i class="fa-lg far fa-square-minus"></i>` --exclude` | A text file containing sample names (one per line) to exclude from the analysis <br/>**Type:** `string` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> TBProfiler Profile Parameters
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --call_whole_genome` | Call whole genome <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --mapper` | Mapping tool to use. If you are using nanopore data it will default to minimap2 <br/>**Type:** `string`, **Default:** `bwa` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --caller` | Variant calling tool to use <br/>**Type:** `string`, **Default:** `freebayes` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --calling_params` | Extra variant caller options in quotes <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --suspect` | Use the suspect suite of tools to add ML predictions <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_flagstat` | Don't collect flagstats <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_delly` | Don't run delly <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-italic"></i>` --tbprofiler_opts` | Extra options in quotes for TBProfiler <br/>**Type:** `string` |
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### <i class="fa-xl fa-solid fa-gears"></i> Optional Parameters

‎docs/bactopia/merlin.md

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| <i class="fa-lg fa-solid fa-toggle-on"></i>` --typing_only` | agr typing only. Skips agr operon extraction and frameshift detection <br/>**Type:** `boolean` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> ClermonTyping
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-file-alt"></i>` --clermon_threshold` | Do not use contigs under this size <br/>**Type:** `number` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> ECTyper
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --hamming` | Report the results as hamming distances <br/>**Type:** `boolean` |
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### <i class="fa-xl fas fa-exclamation-circle"></i> TBProfiler Profile
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| Parameter | Description |
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|:---|---|
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --call_whole_genome` | Call whole genome <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --mapper` | Mapping tool to use. If you are using nanopore data it will default to minimap2 <br/>**Type:** `string`, **Default:** `bwa` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --caller` | Variant calling tool to use <br/>**Type:** `string`, **Default:** `freebayes` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --calling_params` | Extra variant caller options in quotes <br/>**Type:** `string` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --suspect` | Use the suspect suite of tools to add ML predictions <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_flagstat` | Don't collect flagstats <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --no_delly` | Don't run delly <br/>**Type:** `boolean` |
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| <i class="fa-lg fas fa-italic"></i>` --tbprofiler_opts` | Extra options in quotes for TBProfiler <br/>**Type:** `string` |
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## Citations
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If you use Bactopia and `merlin` in your analysis, please cite the following.
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