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genotyphi

Tags: salmonella-typhi genotyping lineage amr mykrobe bactopia-tool

Salmonella Typhi genotyping with lineage assignment.

This Bactopia Tool uses GenoTyphi to call Typhi lineages, AMR determinants, and plasmid markers in Salmonella Typhi samples. Samples are first processed by Mykrobe using mykrobe predict with typhi specified as the species. Then the Mykrobe results are processed by the GenoTyphi parse_typhi_mykrobe.py script.

Usage​

Bactopia CLI:

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

Nextflow:

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

Outputs​

Expected Output Files​

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

Per-Sample Results​

FileDescription
*.jsonMykrobe prediction results
*.tsvGenoTyphi parsed results

Merged Results​

FileDescription
genotyphi.tsvMerged TSV file containing GenoTyphi 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
genotyphi-dag.dotThe Nextflow DAG visualization
genotyphi-report.htmlThe Nextflow Execution Report
genotyphi-timeline.htmlThe Nextflow Timeline Report
genotyphi-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

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

ParameterTypeDefaultDescription
--bactopiastringThe path to bactopia results to use as inputs

Mykrobe Parameters​

ParameterTypeDefaultDescription
--mykrobe_speciesstringSpecies panel to use (choices: sonnei, staph, tb, typhi)
--mykrobe_optsstringExtra Mykrobe options in quotes

GenoTyphi Parameters​

ParameterTypeDefaultDescription
--genotyphi_mykrobe_optsstringExtra Mykrobe options in quotes
Filtering Parameters

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

ParameterTypeDefaultDescription
--includestringA text file containing sample names (one per line) to include from the analysis
--excludestringA 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
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsbooleanList the available workflows and Bactopia Tools to use with '--wf'
--help_allbooleanAn alias for --help --show_hidden_params
--versionbooleanDisplay version text.

Composition​

This workflow uses the following subworkflows:

  • genotyphi - Assign genotypes to Salmonella Typhi genomes.

Citations​

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

Source​

View source on GitHub