As we saw previously, a workflow in the "Workflow management" toolkit is essentially a list of tasks that you chain together to achieve a goal. This concatenation of tasks could be used many times by all the members of a lab group once it is defined beforehand. Thus, a workflow definition was thought of as a useful template with pre-determined tools in direct interaction with the inventory and the machines (data tables, resources and worklists) to optimize the real workflows in your laboratory. 

To start defining a workflow, click on the "Workflow management" option in the main left menu. Then click on the “New Workflow Definition” option:

The image below shows the Workflow Definition view. Here, you can define a workflow in three simple steps:  

1. Add a title to your workflow definition by clicking on the "Untitled Workflow Definition" area and typing in a descriptive name. 

2. Just below, you can write a short description of the new workflow by clicking on the "Workflow Definition Description" area. 

These two steps are not mandatory, but they are necessary for later identification and "execution."

3. You concretely perform the definition by clicking the “Add Task” button, this will open a pop-up window like the one shown in the image below. Here you can choose among a variety of predetermined tools. Scroll down until you find the tool you need or you can search for a specific one by entering a keyword in the field with the magnifying glass icon, to add the tool just click on it.

It is important to note that all these tools can also work independently and can be accessed from the tool library by clicking the "Tools" category on the top menu bar. For more information about the tools, you can visit this collection of our base knowledge. 

The order in which the tasks are added determines the order in which they will be executed, but if you want to rearrange that order, simply click and drag the task you want to move up or down in the list on the right side. You can also delete a task you already added by clicking the trash icon next to it. 

Once you have added all the necessary steps to your list, click "Submit."

The order of the tasks establishes the relationship between their outputs and inputs and you can also setup in advance which output from a previous tool each subsequent tool will use as input. Let’s see that in detail with the hypothetical GGA workflow. 

In this case, the input to start the workflow is a DNA assembly report for further amplification by PCR: 

As you can see in the image below, the “PCR Planning and Inventory Check” outputs are actually the inputs to perform the “Run PCR” task. Generally, for each step, you can choose the sources (Data Tables, DNA Assembly Reports, Reactions Maps, Plates, and Worklists) from which each tool takes the data and performs the task. You can select the “User Defined” option and choose manually or upload the data when you run the workflow. Alternatively, you can select the “Preset” option and indicate the sources beforehand. Every change you make while setting up your workflow definition will be automatically saved, actually you'll see a “Saved” pop-up notification in the upper right-hand corner.

It's important to notice that when a workflow definition is being used by a workflow run it gets locked, which means that you can’t edit or delete it, but you can always create a duplicate and redefine this one. In order to do that click the “Duplicate” button located at the top right and edit this new template just as we have seen so far.

You can preset some of the inputs to be collected from previous steps. In this case, the "Run PCR" task will use the List of Existing Primer PCR Materials, generated as output in the “PCR Planning and Inventory Check”

Note: when a task outputs a worklist, you'll see the yellow warning that indicates it needs to be linked to an "Execute worklist" task.

As soon as you preset the worklist in the "Execute Worklist" task, the warning will disappear.

Once you complete and verify all these aspects of the workflow configuration, you finally have a workflow definition available for infinite runs. The only difference between workflow executions is the data that gets passed through the tasks.

Now, to actually perform this workflow, go to the "Workflow Management" option in left menu bar and select "Workflow Runs." Then click the “New Workflow Run” button and choose this new template in the "Workflow" option. If you need guidance, we will address how to proceed with the "Workflow Run" article.