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Bactopia Tool - mlst

The mlst module uses mlst scan assemblies and determine the sequence type. It makes use of PubMLST schemes and by default automatically scans each schema. To specify a specific scheme to scan, you can provide it with --scheme.

Example Usage

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

Output Overview

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

│   ├── <SAMPLE_NAME>.tsv
│   └── logs
│       └── mlst
│           ├── nf-mlst.begin
│           ├── nf-mlst.err
│           ├── nf-mlst.log
│           ├── nf-mlst.out
│           ├──
│           ├──
│           ├── nf-mlst.trace
│           └── versions.yml
├── logs
│   ├── 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
│   ├──
│   ├── mlst-report.html
│   ├── mlst-timeline.html
│   └── mlst-trace.txt
├── mlst.tsv
├── software_versions.yml
└── software_versions_mqc.yml


Top Level

Below are results that are in the base directory.

Filename Description
mlst.tsv A merged TSV file with mlst results from all samples


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

Filename Description
<SAMPLE_NAME>.tsv A tab-delimited file with mlst result, see mlst - Usage for more details

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
mlst-report.html The Nextflow Execution Report
mlst-timeline.html The Nextflow Timeline Report
mlst-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

MLST Parameters

Parameter Description Default
--scheme Don't autodetect, force this scheme on all inputs
--minid Minimum DNA percent identity of full allelle to consider 'similar' 95
--mincov Minimum DNA percent coverage to report partial allele at all 10
--minscore Minumum score out of 100 to match a scheme 50
--nopath Strip filename paths from FILE column False

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 mlst in your analysis, please cite the following.