Fig 1.
Configuration of workflows is done once through the workflow admin panel in qPortal. Besides the name, version, and a description of the worklfow, associated experiment and samples types in openBIS have to be selected. Workflow runs and their results will be stored in the database as data and meta information. Additionally, the parameters of the workflow which will be shown to the user can be selected (highlighted in blue in this example).
Fig 2.
qPortal is connected to openBIS and the workflow engine. The workflow engine is connected to a high-performance computing cluster. Users may create projects, upload their data (Datamover), and analzye it through qPortal (Project Wizard and Project Browser). Results are automatically written back to the database and presented on the portal (Project Browser).
Fig 3.
The main view of the Project Browser shows general information about the project such as the name, description, investigators, and a status. Users can navigate to other views like the project graph, available datasets, and the workflow submission view by clicking on the corresponding tabs.
Fig 4.
qPortal consists of several software components which have been implemented. The Java library Liferay Utils is connected to each portlet and ensures authentication of users and enables Liferay functionality for our portlets Project Wizard and Project Browser. These provide users with means of project creation and management via another Java library wrapping the openBIS API (openBIS Client). Import, configuration and submission of workflows via the communication with the gUSE API and openBIS is handled by our implemented Java library Workflow Handler. Java libraries are shown in dashed line boxes whereas the two presented main portlets of qPortal are shown in regular boxes.
Fig 5.
One part of the project registration through the Project Wizard as first step of the project management workflow realized by qPortal: values of the experimental design variables ethnicity and sex are input by the user. Resulting combinations are shown and can be adjusted by the user.
Fig 6.
Workflow selection and submission.
All available workflows for the corresponding project can be seen in the workflow tab. After selecting the workflow, users select input files and specify the parameter values. If the submission was successful, users will be notified.
Fig 7.
Results of workflow runs will be directly visualized in qPortal. In this case results of one OptiType and one FastQC run are visualized.