How to generate the json files for Cromwell workflow execution?
Unfortunately generating inputs for Cromwell is not something that is handled by Cromwell itself or by GATK, and generally needs to be scripted to fit your custom needs. 

Despite this being a bit arduous, there is a very good reason for this. WDL itself is a highly polymorphic workflow language, where inputs can be vastly different between each workflow. Cromwell ONLY understands how to parse the workflow and the inputs, but does not know the context of what it is running (ie this is a paired mapping job), nor does GATK know that it is running within a WDL. 

Additionally, I've encountered many different cases where there are not just 2 fastq files but, due to older sequencing technologies, 10 or more for the same sample. Unless GATK/Cromwell knows how your specific samples are arranged there is no easy way for them to generate your inputs.

There are tools that would possibly help you simplify scripting better. WOMTool developed by the Broad has an inputs command which will take an  arbitrary workflow and generate a JSON template of the inputs, which you can then use in your own scripts. 

As an example, imagine you have this WDL workflow in a file called my.wdl:

version 1.0
workflow foo {
  input {
    Array[Pair[File,File]] fastqFiles
  }
}


When you run WOMtool's inputs command, it produces a template JSON listing all inputs and specifying the variable types expected for each:

$ java -jar womtool.jar inputs my.wdl
{
  "foo.fastqFiles": "Array[Pair[File, File]]"
}


You can use this template to produce actual JSONs for each of your samples.

Note that you can also get the template written to a file as follows: 

$ java -jar womtool.jar inputs my.wdl &gt; my.inputs.json