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.

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

Results¶

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

mlst¶

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.

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
mlst-dag.dot	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

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

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¶