Every analysis in DNAnexus is run using apps. Apps can be linked together to create workflows.
The Tools Library shows a complete list of apps and workflows available to you. Use filters to quickly find items by name, category, etc. The "pin" feature allows you to mark your favorite tools and they will remain on top of the list. The "info" panel gives you quick access to view app inputs and outputs.
To learn more about a particular tool, click its name. This opens the full information page which contains details about inputs, outputs and what's under the hood. For apps encapsulating existing bioinformatics tools this page also contains licensing information, links to the website for that software, and citations to any related publications. Additional tabs show the version history for the app and developer documentation which describes the inner workings of the app in detail.
Apps and workflows can be run from either the main Tools Library page from within a specific project. The tools default to place output objects in the same project.
In the Manage view for a project, there are two options:
Run -- This enables you to pick a single app to run, or to create a single-use disposable workflow.
New Workflow -- This creates a new workflow capable of running multiple stages of apps. This enables you to string together multiple analysis steps that depend on each other.
Each application runs on a cloud-specific DNAnexus instance type.