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 14.26). A page symbol on the right hand side of the middle section of a workflow element indicates the element can be configured.
Figure 14.26: Anatomy of a workflow element
Workflow element coloring
Workflow elements are colored according to their category (figure 14.27). The default colors are:
- 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.
- Purple
- 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.
Element colors can be changed under the Element style palette in the Side Panel of the editor.
The name of a new element added to a workflow is shown in red text until it is connected to other elements.
Configuring Input and Output elements is described in Configuring Workflow Input elements and Configuring Workflow Output and Export elements.
Control flow elements are described in Batching part of a workflow.
Figure 14.27: The coloring of the elements indicates that "Annotate with GFF/GTF/GVF files" is a tool with at least one setting with a non-default value, "Create Alignment" is a tool where all settings have default values, "Workflow Input" is an Input element with default settings, and the two elements connected to the Alignments channel are an Output and an Export element, both with default settings.