Here are a few general pointers about the graphical workbench clients and the command line tools client and which of the two types of clients to choose.
Scripting pipelines
The command line tool is ideal for scripting pipelines of data analyses. By encapsulating the instructions to the server in a script, you can run all your data sets through the same pipeline of analyses, making this a consistent and effective framework for production settings. The Workbench can be very useful as a companion to the CLC Command Line tools, for exploring the analyses available, running initial pilot tests, determining appropriate parameter settings, deciding on quality control steps, and so on. The Workbench is also ideal for graphical investigation of results. After an analysis pipeline has been finalized, a series of CLC Command Line Tool calls making up the analysis pipeline can be defined in a script.
Workflows
Workflows installed on CLC Servers can be launched via CLC Command Line Tool calls. Defining workflows should be done using the Workflow editor within a CLC Workbench.
Visualization and interpretation
Visualization and interpretation of results would usually be done with a CLC Workbench. Results can also be exported to standard formats for downstream analysis or viewing using other applications.
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