Batch processing refers to running an analysis multiple times, using different inputs for each analysis run. For example, if you have 10 sequence lists and wish to run 10 mapping analyses, one per sequence list, then these 10 analyses could be launched by setting up one batch job. When a job is run in batch mode, parameter settings stay the same for each run. It is just the inputs that are changed.
You can read more about how to run workflows individually or in batch mode here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html
Information about launching a workflow with more than one input, where the contents of more than one input should change in each batch, is provided here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Batching_workflows_with_more_than_one_input_changing_per_run.html
An example of how to launch such a workflow in batch mode is provided for the Perform QIAseq Multimodal Analysis ready-to-use workflow in Perform QIAseq Multimodal Analysis (Illumina) ready-to-use workflow.