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 customizable since users can define input data, configure the parameters of each step, save and export results, generate charts and statistics and more.
Figure 1: Workflow Composer Interface
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.
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.
Figure 5: Input data definition
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.
Figure 6: Output data definition
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).