Samtofastq Method Config.

Hi,
I am new to FireCloud. I was wondering if it is possible to revert BAMs to FASTQ, then merge multiple FASTQ from different runs for one sample, and then align back - all in FireCloud. I first tried the existent Samtofastq method configuration on FireCloud but I don't seem to be able to write the appropriate metadata file to run it because I cannot find how to write it up. I do not want to write my own WDL, I just want to use the method configuration that exists already.
Thank you in advance for any help.