Workflows

Introduction

OmicsBox provides an interface to create, edit and run workflows based on the Common Workflow Language (CWL) specification. This interface allows to describe all analysis steps using the functions and tools offered by OmicsBox and connect them to perform a complete analysis in a single run. Workflows are highly customisable since users can define input data, configure the parameters of each step, save and export results, generate charts and statistics and more.

Workflow Composer

The OmicsBox workflow composer interface offers all the necessary options to manage workflows. You can access the composer using the "Workflows" toolbar item or the "Create Workflow" menu option in the workflows toolbar menu.

Using the "Properties" button in the side panel it is possible to edit the documentation of the workflow. You can write whatever information it is useful, like the author name, author email and a description of the workflow.

**Figure 2:**List of actions that can be included in a workflow

Design Workflows

To create a workflow, start adding some steps. The side panel (on the left) contains the list of actions (that may vary depending the apps installed in OmicsBox) that can be used as workflow steps (Figure 2). To add an action to the workflow click on the corresponding plus symbol next to the action's name.

Each action is represented by an icon (Figure 3). On the left side of the icon are placed the connections for every input of the action (e.g. project, count table, etc) and on the right side are placed the connections for every output it produces as result (chart, graph, etc).

To connect two steps of the workflow, click on the small circle representing the output connection of the first action and drag it to the small circle representing the input connection of the second action. If the connection is valid (i.e. both types match) the small input connection circle should turn green, and a line connecting both circles should be displayed. Otherwise, the small input connection circle should turn red, indicating the selected output can not be used as input for that action.

Configure workflow steps

Most workflow steps can be configured. If a step needs to be configured (because its parameters are not valid) it will be highlighted in red color and it will not be possible to run the workflow (Figure 4). To configure the step right-click on the step icon and select the "Edit Parameters" option. The red color should disappear as the parameters are now valid. The parameters of each step can be consulted in the bottom region of the side panel.

**Figure 4:** Valid step (left), invalid step (right).

Define workflow inputs

Workflow inputs are .b2g files by definition. To use a .b2g file as input click on the input connection on the left side of the icon and drag it out. The input file can be selected by right-clicking on this step and selecting the "Select Input File" option (Figure 4 top) or in the "Run Workflow" wizard.

Some actions don't require any input and produce a result that can be used as input by other actions. These actions can be incorporated as first step in a workflow (e.g. Load Fasta, Eukaryotic and Prokaryotic Gene Finding, Create Count Table, etc).

Define workflow outputs

Like inputs, workflow outputs are .box/.b2g files by definition. To save the results as .box/.b2g files click on the output connection on the right side of the icon and drag it out. The output name (file name in the end) can be selected by right-clicking on this step and selecting the "Change Output Name" option (Figure 6). Later in the "Run Workflow" wizard it is possible to choose the output folder of every output, or use a common output folder for all workflow's outputs.

If you want to export the output of a workflow as a regular file (e.g. .txt, .csv, .png) instead as .box/.b2g file, use the several export actions to export annotations, charts and statistics that OmicsBox offers. These actions can be incorporated as the last step in a workflow (e.g. Generic Export, Export Chart, Export Report, etc).

Run workflows

Once the workflow is ready click on the green "Run" button on the side panel to open the "Run Workflow" wizard. Here you can select the inputs files and the outputs folder(s) to save the results or use a common folder for all results (Figure 7). Click "Run" to execute the workflow. You will see a new progress bar for the workflow execution, and an additional progress bar for every step, so it is possible to cancel the whole workflow or just a certain step and continue with the others.