Anatomy of workflow elements

Workflow elements can pass data to other elements, accept data from other elements, or do both of these. Elements that data can enter into and flow out of consist of 3 regions: input channels at the top, output channels at the bottom, and the core section in the middle where the element name is (figure 14.33). A page symbol on the right hand side of the middle section of a workflow element indicates the element can be configured.

Image element_explained
Figure 14.33: Anatomy of a workflow element.

Workflow element coloring

Workflow elements are colored according to their category (figure 14.34):

Light green
Input elements. Elements for taking in the data to be analyzed.
Dark blue
Output and Export elements. Elements that indicate data should be saved to disk, either in a CLC location (Output elements) or any other accessible file location (Export elements).
Light grey
An analysis element where the default values are used for all settings.
A configured analysis element, i.e. one or more values in that element have been changed from the defaults.
Emerald green
Control flow elements with default settings.
Forest green
Configured control flow elements. i.e. one or more values in that element have been changed from the defaults.

Background colors can be changed under the Design tab in the side panel settings of the Workflow editor.

The name of a new element added to a workflow is shown in red text until it is properly connected to other elements.

Configuring Input and Output elements is described in Configuring input and output elements.

Control flow elements, used to fine tune control of the execution of whole workflows or sections of workflows, are described in Batching part of a workflow.

Image workflow_element_coloring
Figure 14.34: An element's color indicates the role it plays and its state. Here, Trim Reads means is using only default parameter values, whereas the purple background for Map Reads to Reference indicates that one or more of its parameter values have been changed. The green elements are Input elements. The blue color of the InDels element and parts of the Export PDF element indicate that data sent to these elements will be saved to disk.