.. _user_guide:

User Guide
==========

This section provides a comprehensive guide for users to understand how to use the software effectively. It includes detailed instructions, examples, and best practices to help users navigate through the features and functionalities.

.. toctree::
    :maxdepth: 2

    installation_of_required_software
    gpsw_commands
    configuration_of_snakemake
    run_gpsw_with_test_data
    run_gpsw_with_your_own_data
    workflow_settings
    output_files_by_directory