What is are Pipelines in Biztalk Server ?

• The BizTalk adapters take up the responsibility of interacting with the end systems and getting the data. 
• it is the pipelines transform the data into something that BizTalk can understand – Xml.
• pipelines form a channel for the messages from the adapters to the message box where they are finally delivered. After the message leaves the pipeline, the messaging engine is responsible for the further processing of the messages. The processing can include routing or executing a business process – as has been defined by the developer.

 Note :

The messaging engine works on a certain format of data that it terms as a message. This is necessarily a XML message with a specific format containing the message headers and body parts. The Adapter is explicitly responsible for interacting directly with the end systems. To isolate the workload, the adapter does not take care of any kind of formatting of the message so that the message is understood by the Messaging Engine. This is exactly the reason where the pipelines play their role. The pipelines accept the data from the adapters and work on it to build up the Message that can be understood by the messaging engine.

http://blogs.msdn.com/b/sanket/archive/2006/06/13/pipelines-in-biztalk-2006.aspx 

http://www.c-sharpcorner.com/UploadFile/johncharles/89/Default.aspx