Pipeline App Panel
The App Builder tab on the toolbar on the left opens the App Builder. The Pipeline App Builder allows the user to turn their Pipeline into a No-Code App that passes arguments to the command line in each Capsule, and compiles the App Panels from each Capsule in the Pipeline.
To create a Pipeline App Panel, press Create App. Note that this will deactivate the Arguments box in the Capsule Settings.
The App Builder has the following sections:
General: Enter an optional App Subtitle and Instructions for App usage.
Data: Attach one or more Data Assets to the Capsule to specify as default data. These Data Assets can be exchanged for other Data Assets by the user.
Parameters: This section transfers the App Panel from each Capsule to the Pipeline. The order of Capsules can be changed by reordering the cards.
Display result after run: After a run has been performed, the file to display after subsequent runs can be selected.
Once the Pipeline App Panel has been created, you will then be able to name the App, attach default Data Assets (e.g., a human reference genome or annotations), rearrange parameters grouped by Capsules, and save the App.
An example of a completed App Panel for a Pipeline with two Capsules, FastQC and MultiQC is below. Note that the parameters are grouped by Capsule.
