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Bactopia Tool - tbprofiler

The tbprofiler module uses TBProfiler for profiling reads to determine resistance and Mycobacterium tuberculosis strain type.

Example Usage

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

Output Overview

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

tbprofiler/
├── <SAMPLE_NAME>
│   ├── <SAMPLE_NAME>.results.csv
│   ├── <SAMPLE_NAME>.results.json
│   ├── <SAMPLE_NAME>.results.txt
│   ├── bam
│   │   └── <SAMPLE_NAME>.bam
│   ├── logs
│   │   └── tbprofiler
│   │       ├── nf-tbprofiler.{begin,err,log,out,run,sh,trace}
│   │       └── versions.yml
│   └── vcf
│       └── <SAMPLE_NAME>.targets.csq.vcf.gz
├── logs
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions.{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├── tbprofiler-dag.dot
│   ├── tbprofiler-report.html
│   ├── tbprofiler-timeline.html
│   └── tbprofiler-trace.txt
├── software_versions.yml
└── software_versions.yml

Directory structure might be different

tbprofiler 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 tbprofiler directory structure might be different, but the output descriptions below still apply.

Results

TBProfiler

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

Filename Description
<SAMPLE_NAME>.results.csv A CSV formated TBProfiler result file of resistance and strain type
<SAMPLE_NAME>.results.json A JSON formated TBProfiler result file of resistance and strain type
<SAMPLE_NAME>.results.txt A text file with TBProfiler results
<SAMPLE_NAME>.bam BAM file with alignment details
<SAMPLE_NAME>.targets.csq.vcf.gz VCF with variant info again refernce genomes

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
tbprofiler-dag.dot The Nextflow DAG visualisation
tbprofiler-report.html The Nextflow Execution Report
tbprofiler-timeline.html The Nextflow Timeline Report
tbprofiler-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

TBProfiler Parameters

Parameter Description Default
--call_whole_genome Call whole genome False
--mapper Mapping tool to use. If you are using nanopore data it will default to minimap2 bwa
--caller Variant calling tool to use freebayes
--calling_params Extra variant caller options in quotes
--tb_min_depth Minimum depth required to call variant 10
--tb_af Minimum allele frequency to call variants 0.1
--tb_reporting_af Minimum allele frequency to use variants for prediction 0.1
--coverage_fraction_threshold Cutoff used to calculate fraction of region covered by <= this value 0
--suspect Use the suspect suite of tools to add ML predictions False
--no_flagstat Don't collect flagstats False
--no_delly Don't run delly 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.

Citations

If you use Bactopia and tbprofiler in your analysis, please cite the following.