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.
You must set up billing for your account before you can perform an analysis, or upload or egress data. Follow these instructions to set up billing.

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.
On the DNAnexus Platform, apps and workflows are generically referred to as "tools."
To find the tool you're looking for in the Tools Library, you can use search filters. Filtering enables you to find tools with a specific name, in a specific category, or of a specific type:
To see what inputs a tool requires, and what outputs it generates, select that tool's row in the list. The row will be highlighted in blue; the tool's inputs and outputs will be displayed in a pane to the right of the list:
To make sure you can find a tool later, "pin" it to the top of the list. Click the "..." 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 will open, showing a wide range of info, including guidance in how to use it, version history, pricing, and more:

Running Apps and Workflows

Apps and workflows can be launched via the UI in two ways.

Launching from the Tools Library

From a tool's detail page in the Tools Library, you can launch it by clicking the Run button:

Launching from a Project

From within a project, navigate to the Manage pane, then click the Start Analysis button
A modal window will open, showing the same list of available tools you see in the Tools Library. Select the tool you want to run, then click Run Selected:


If the tool needs to be installed prior to being run, you'll be prompted to do so:

Tool Configuration

Before a tool can be run, you need to configure it, providing required inputs, specifying where output files should be placed, and selecting settings. For a tool such as a workflow that has multiple stages, you'll need to configure each stage as well.
Enter all configuration information on the UI tool runner page, via the fields in the Analysis Settings, Analysis Inputs, and Stage Settings panes:
Analysis Settings - Specify a name for the job, the project in which it will run, and the folder in which output files will be stored. Optionally, set the job's priority to "high" vis-a-vis other jobs being run on the system, and set a spending limit for the job. If you are a member of an org for which Job Ranking has been enabled, you will see a Job Ranking field. Enter a value to set the priority given to this job relative to others, in restarting jobs once workers become available, after your worker limit is reached.
A license is required to use the Job Ranking feature. Contact DNAnexus Support.for more information.
Analysis Inputs - The list of inputs will be specific to the tool. Fields for required inputs are marked with an asterisk (*). If you are processing multiple files in a batch run, click the Enable Batch toggle. See the next section for more on batch runs.
Stage Settings - View the tool's version number, and the instance type, and output folder, it uses by default. Optionally, change the instance type or select custom output folders.

Batch Runs

Setting Up a Batch Run for Multiple Files

Click the Enable Batch toggle to set up a batch run:
Click the "file" icon next to the input for which you want to use multiple files. The input will turn purple:
Click the input bearing the label Configure Batch to open the Configure Batch Inputs screen.
On that screen, click the Add Files to Batch button to select files. Selected files will appear in the left-side pane. Initially, each will be labeled "Unused." To add one of these files as an input, drag it to the right-side pane, dropping it on the target. Note that the target will initially bear the label "Not Configured":
You can also choose a pattern from the dropdown in the Patterns field, to automatically add, as an input, one or more of the selected files that match the selected pattern.
To return to the Analysis Settings pane and complete setup, click the Complete Changes 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, leveraging advanced techniques like smart reuse.