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What's the best way to process multiple samples in "Data pre-processing for variant discovery"

In the Best Practice "Data pre-processing for variant discovery," the json file include parameters PreProcessingForVariantDiscovery_GATK4.sample_name and PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list. The flowcell_unmapped_bams_list is mean for include multiple bam files from the same sample, and sample_name is for the actual sample name. So this pipeline can only process one sample per run.

My question is how to or is there a way to parameterized this pipeline to process multiple samples in one call? Or how to integrate this pipeline into a script to process multiple samples? For example, is it possible to give the sample_name a value like $NAME and get the actual sample name from a shell variable? How about the flowcell_unmapped_bams_list?

Thank you very much for the help!

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