Execute apps on CAVATICA to perform analyses. Each app execution is called a task. Each task is associated with a set of input files and chosen settings for the tool(s) in the app.
On this page, learn about the different types of tasks as well as the configurable components of a task.
Conversely, see the step-by-step instructions for running a task.
A task is an execution of an app. Each task is associated with a set of input files and parameter settings. There are two types of tasks on CAVATICA:
- Single task: A single task represents one execution of a workflow or tool in your project.
- Batch task: Batch tasks comprise of several child tasks and are used to run the same workflow or tool multiple times with varying inputs in parallel executions. Learn more about batch tasks.
While you set up a task, it is in a draft state and is labelled DRAFT. Each DRAFT task is saved in the Tasks tab for you to set up and run whenever convenient.
Learn how to create a DRAFT task as part of running an analysis.
Input files are the data on which you execute your analysis.
Note that before you configure your task, input must have already been added to your project. You can add files to a project from the Public Files Repository, from another project, or by uploading them directly to your project.
Learn about specific types of input files below. Or, learn how to select input files as part of running your analysis.
A reference file is a specific type of input. CAVATICA maintains the latest and the most frequently used reference genomes and annotation files in its Public Reference Files repository, so you won't have to upload your own reference files each time.
To help you get started with your analyses, some of the public workflows in the Public apps gallery have suggested reference files. This feature allows you to easily add the necessary reference files to help your workflow run properly.
A Suggested files pop-up will prompt you to add the suggested files when setting up your draft task.
If you already have all the suggested reference files in your project, they will pre-populate your draft task page. If any of your workflow's suggested files are not in your project, a Suggested files pop-up will prompt you to copy the missing files to your project. You can:
- Populate your task with the suggested files by clicking Copy.
- Ignore the suggested files by clicking Don’t copy. The pop-up is permanently dismissed and you can choose your own reference files.
- Postpone your decision by closing the Suggested files pop-up. The pop-up will appear again the next time you access this draft task.
The App Settings section under the Task Inputs tab on the draft task page allows you to set the exposed parameters for every tool in your app. For information on exposing parameters, see the documentation on editing an app.
Only parameters marked to be exposed at runtime can be edited, but you can view all tool parameters. The View Parameters dropdown list allows you to:
- Show all - Displays all editable and non-editable parameters.
- Show editable - Displays editable parameters in view mode.
- Show non-default - Displays parameters whose values have been modified compared to the default ones.
Learn how to define app settings as part of running your analysis.
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