7.1 Syncing Execution Flow
If your pipeline requires the sequential execution of modules, but the modules do not have any dependencies on each other to regulate the ordering of the execution, then there is a way you can construct your workflow to preserve the order of execution. Let us look at a concrete example.
Module A generates an output file, which is used by both Module B and Module C. However, Module B and Module C has an “implicit dependency”, meaning that although there is no explicit input/output file passing between these two modules, Module C has to be executed after Module B is complete. This is illustrated on the left.
The workflow above will not guarantee Module C executed after Module B is done. As soon as Module A finishes, Module B and C will start. To solve this, there are two ways.
Make a flow control connection between Module B and C that will force Module C to wait until Module B completes. In order to configure the a flow control connection, add a new output parameter of Module B, specify it as type Flow Control. Next, add a new input parameter of Module C, specify it as type Flow Control too. Connect these two parameters and you are done. See the modified workflow on the left (the flow control connection is highlighted).
Alternatively, you create a new output parameter of Module B of type File, with the number of arguments at 0. Next, create a new input parameter of Module C of type File, also with the number of arguments at 0. Connect these two parameters. See the modified workflow on the left (the connection is highlighted).
7.2 Exporting Pipeline Workflow to Script
All Pipeline workflows (.pipe files) may be executed in a batch mode without involving the LONI Pipeline graphical user interface (GUI). This enables trivial inclusion of pipeline protocols in external scripts and integration into other applications. Currently, the LONI Pipeline allows exporting of any workflow from XML (*.pipe) format to a makefile or a bash script for direct or queuing execution.
Simply open up any workflows, make changes if necessary, and choose File -> Save As… Choose a folder and specify file name and file format and Pipeline will export this wrokflow to your desired format.
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