Connecting workflow elements

Figure 9.7 explains the different parts of a workflow element.

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Figure 9.7: A workflow element consists of three parts: input, name of the tool, and output.

At the top of each element a description of the required type of input is found. In the right-hand side, a symbol specifies whether the element accepts multiple incoming connections, e.g. +1 means that more than one output can be connected, and no symbol means that only one can be connected. At the bottom of each element there are a number of small boxes that represent the different kinds of output that is produced. In the example with the read mapper shown in figure 9.2, the read mapper is able to produce a reads track, a report etc.

Each of the output boxes can be connected to further analysis in three ways:

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Figure 9.8: Dragging the reads track output with the mouse.

Image workflow_connect_drag_end
Figure 9.9: The reads track is now used for variant calling.

All the logic of combining output and input is based on matching the type of input. So the read mapper creates a reads track and a report as output. The variant caller accepts reads tracks as input but not mapping reports. This means that you will not be able to connect the mapping report to the variant caller.