Workflow Designer: Pipelines and Repeatable Experiments

Workflow Designer. UGENE Workflow Designer is a central part of UGENE that allows a molecular biologist to create and run complex computational workflows, even if they are not familiar with any programming language.

A workflow comprises a reproducible, reusable, and self-documented research routine, with a simple and unambiguous visual representation suitable for publications. A workflow can be run both locally and remotely, either using a graphical interface or launched from the command line. Elements in the workflow correspond to algorithms integrated into UGENE. Additionally, you can create custom workflow elements using an integrated scripting language or by connecting arbitrary external command line utilities.

To launch the Workflow Designer, select the Tools ‣ Workflow Designer item in the UGENE main menu. The following window appears:

Example 4: You can find a pattern in a sequence or sequences and save it as annotations using the following workflow:

Create the workflow, choose parameters, and click the Run button. If you want to search for patterns in many sequences, you can add these sequences into the Read Sequence element. After the process ends, a report appears. The report includes all information about the workflow.

All your workflows are saved, and you can navigate between them and use them with the help of the Dashboards Manager:

Note that workflows in UGENE are easy to read and share, can be reused multiple times, and compiled into separate standalone command line tools!

For more detailed information about the Workflow Designer, use the Workflow Designer Documentation.