This repository contains the main scripts for routine analysis of clinical next generation sequencing (NGS) data at Viapath Genetics. Follow the links in the below table for specific documentation.

Each runfolder must be discrete per workflow, therefore must consist of only one of the following types:

• TSO500
• ADX
• SNP
• WES
• Custom Panels / LRPCR
• ONCODEEP
• DEV (with or without UMIs)

The type of run is detected by the scripts by matching the Pan numbers within the sample names in the corresponding samplesheet to the pan numbers in the panel_config.

The script has been tested using python v3.10.6 therefore it is recommended that this version of python is used.

Dependencies, which include the samplesheet_validator package**, are installed using the requirements.txt file:

pip3 install -r requirements.txt

Before running the script, the conda environment must be activated as follows:

conda activate python3.10.6

** The samplesheet_validator package validates naming and contents of samplesheets prior to demultiplexing, using the seglh-naming package (guide).

The config directory contains configuration files. See (guide). for further details.

The below diagram is a UML class diagram showing the relationships between the classes in this repository. Classes are colour-coded by modules. Per-module documentation is available within each module directory.

Class and package diagrams were generated by running the following command from the project root:

pyreverse -o png -p automate_demultiplex . --ignore=test --source-roots . --colorized --color-palette=#CBC3E3,#99DDFF,#44BB99,#BBCC33,#EEDD88,#EE8866,#FFAABB,#DDDDDD,#eab676 --output-directory img/

The above image describes the possible associations in the Class Diagram. In the classes in this repository we have the following associations:

test contains test data (/test/data), and test scripts within individual modules (these use pytest).

Tests can be executed using the following command. It is important to include the ignore flag to prevent pytest from scanning for tests through all test files, which slows down the tests considerably

python -m pytest

Currently test suite coverage is as follows:

Total coverage: 45% (N.B. this includes all scripts incl init and main scripts)

TESTS AND TEST CASES/FILES MUST BE MAINTAINED AND UPDATED ACCORDINGLY IN CONJUNCTION WITH SCRIPT DEVELOPMENT

Tests should be run before pushing any code to ensure all tests in the GitHub Actions workflow pass.

In production mode, alerts are sent to the moka-alerts binfx slack channel, whilst in testing mode they are sent to the moka-poo slack channel.

Alerts at level ERROR and above will appear in the relevant channel.

Scripts are triggered by a cronjob on the linux workstation which can be updated using sudo crontab -e.