The Tools Library under the Tools tab of the platform shows a complete list of apps and workflows available to you. Use filters to quickly find items by name, category, etc. The Add Pin button allows you to mark tools and places them at the top of the library. Clicking the bar containing the app name opens up a panel on the right side of the screen that shows you the inputs and outputs of that app.
Clicking on the name of the app will open up a separate information page which contains details about the app's inputs, outputs, and other documentation details. 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. This page also shows 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 the section Batch Runs 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.