Pipelines are meant for pre or post-processing of messages as they enter or leave BizTalk Server. They are used to perform specialized tasks, splitting or aggregating a message, are executed between the Adapter and the Map vice versa for Send Ports.
The Receive pipeline has 4 stages: Decode, Disassemble, Validate & Resolve. Are meant for preprocessing the message such as parsing a Flat File or XML file.
The Send pipeline has 3 stages: Pre-Assemble, Assemble & Encode. Are meant for post-processing the message before it gets sent out by the adapter.
When you install BizTalk Server, you will get by default to 4 Pipelines, 2 Receive & 2 Send. They have no components and performs no message.
You can develop Custom Pipelines using Visual Studio Pipeline Designer.