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:
Start Analysis -- This enables you to pick an app or workflow to run.
New Workflow -- This enables you to create a new workflow capable of running multiple stages of apps. You can string together multiple analysis steps that depend on each other.
Each application runs on a cloud-specific DNAnexus instance type.
Analysis Settings - Select a name, project and output folder.
Analysis Inputs - Required inputs are indicated with an asterisk (*). Turn on batch from here. (see below for more info)
Stage Settings - View version number, instance type and output folder. You can change the instance type here or select custom output folders for each stage.
Turn on enable batch to allow for selecting multiple files as inputs.
Click the file icon next to the input that you want to enable batch for (it will turn purple).
Click configure batch to select files.
Add your files by clicking add files to batch and they will appear on the left side
Either drag the files to the right side list, or choose a pattern from the menu to automatically assign input files.
Click complete changes to proceed.