Apps and Workflows
Every analysis in DNAnexus is run using apps. Apps can be linked together to create workflows. Learn the basics of using both.
Finding the Right App or Workflow
The Tools Library provides a list of available apps and workflows. To see this list, select Tools Library from the Tools entry in the main Platform menu.
To find the tool you're looking for in the Tools Library, use search filters to narrow the list by name, category, or type:
To see what inputs a tool requires, and what outputs it generates, select that tool's row in the list. The row is highlighted in blue. The tool's inputs and outputs are displayed in a pane to the right of the list:
To make sure you can find a tool later, you can pin it to the top of the list. Click the More actions (⋮) icon at the far right end of the row showing the tool's name and key details about it. Then click Add Pin.
To learn more about a tool, click on its name in the list. The tool's detail page opens, showing a wide range of info, including guidance on how to use it, version history, pricing, and more:
Running Apps and Workflows
Launching a Tool
Launching from the Tools Library
You can launch the latest version of any given tool from the Tools Library page. Or you can navigate to the app details and click Run.
Launching from a Project
From within a project, navigate to the Manage pane, then click the Start Analysis button.
A dialog window opens, showing a list of tools. These include the same tools as shown in the Tools Library, as well as workflows and applets specifically available in the current project. Select the tool you want to run, then click Run Selected:
Workflows and applets can be launched directly from where they reside within a project. Select the workflow or applet in their folder location, and click Run.
Launch Configuration
Confirm details of the tool you are about to run. Selection of a project location is required for any tool to be run. You need at minimum Contributor access level to the project.
Configure Inputs and Outputs
The tool may require specific inputs to be entered before starting the run. You can identify the required inputs by looking for the highlighted areas that are marked Inputs Required on the page.
You can access help information about each input or output by inspecting the label of each item. If a detailed README is provided for the executable, you can click the View Documentation icon to open the app or workflow info pane.
To configure instance type settings for a given tool or stage, click the Instance Type icon located in the top-right corner of the stage.
To configure output location and view info regarding output items, go to the Outputs tab under each stage. For workflows, output location can be specified for each stage.
The I/O graph provides an overview of the input and output structure of the tool. The graph is available for any tool and can be accessed via the Workflow Actions menu.
Once all required inputs have been configured, the page indicates that the run is ready to start. Click on Start Analysis to proceed to the final step.
Configure Runtime Settings
As the last step before launching the tool, you can review and confirm specific runtime settings, including execution name, output location, priority, job rank, spending limit, and resource allocation. You can also review and modify instance type settings before starting the run.
Once you have confirmed final details, click Start Analysis to start the run.
Batch Run
Use batch run to launch the same app or workflow multiple times with different inputs for each run.
Specify Batch Inputs
To enable batch run, start from any input that you want to specify for batch run, and open its I/O Options menu. From the list of options available, select Enable Batch Run.
Input fields with batch run enabled are highlighted with a Batch label. Click any of the batch enabled input fields to enter the batch run configuration page.
Files and other data objects
Yes
Files and other data objects (array)
Limited support. Accepts a single-value array.
String
Yes
Integer
Yes
Float
Yes
Boolean
Yes
String (array)
No
Integer (array)
No
Float (array)
No
Boolean (array)
No
Hash
No
Configure Batch Inputs
The batch run configuration page allows specifying inputs across multiple runs. Interact with each table cell to enter values for any run or field.
Similar to the configuration of inputs for non-batch runs, you need to complete all the required input fields to proceed to the next steps. Optional inputs, or required inputs with a predefined default value, can be left empty.
Once all required fields (for both batch inputs and non-batch inputs) have been configured, you can proceed to start the run via the Start Analysis button.
Starting and Monitoring Your Analysis
Once you've finished setting up your tool, start your analysis by clicking the Start Analysis button. Follow these instructions to monitor the job as it runs.
Learn More
Learn in depth about running apps and workflows, using advanced techniques like Smart Reuse.
Learn more about building apps using Bash or Python.
Learn in depth about building and deploying apps, including Spark apps.
Learn in depth about importing, building, and running workflows.
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