Documentation Overview

The current documentation of NovaScope include the following sections:

Home:

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

Installation:

• Installing NovaScope: Details of installing required softwares and acquiring reference database.
• Environment Setup: Outlines how to prepare a configuration file for computing environment.
• Slurm: (Optional) Guidance on setting up a configuration for the SLURM job scheduler.

Getting Started:

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

NovaScope Walkthrough:

• A Rule Execution Guide: Essential concepts and rule execution flows by request.
• Specific Rule Instructions: Detailed instructions for all rules.