Documentation Overview

The current documentation of NovaScope includes the following sections:

Home:

• Documentation Overview: Contents and structure of this documentation.
• Workflow Structure: Describes NovaScope's workflow, including rules and their dependencies.

Installation:

• Installing NovaScope: Details the installation of required software and the acquisition of reference databases.
• Additional Installations: (Optional) Instructions for installing tools for NovaScope's additional functionalities.
• Environment Setup: Outlines how to prepare an environment configuration file for the computing environment.
• SLURM: (Optional) Guidance on setting up a configuration for the SLURM job scheduler.

Basic Usage:

• Introduction: A quick introduction to using NovaScope with example datasets.
• Accessing Input Data: Information on accessing three provided example datasets.
• Job Configuration: Instructions for preparing a job configuration file.
• Execute NovaScope: Describes three ways to run NovaScope.
• Output: Explains the output directory structure and how to utilize the generated data.

Full Documentation:

• A Rule Execution Guide: Essential concepts and rule execution flows by request.
• Main Rules: Detailed instructions for rules serving the main functionalities.
• Plus Rules: Detailed instructions for rules serving the additional functionalities.