This reverts commit eec323ef.

  Virtual memory usage in Shark Cluster at LUMC is considerably more than in local testing.
  CombineVariants command had to be updated because "-o pipefail" is not a recognized option in Shark computing nodes. Also, because the cromwell config uses "sh" to run the scripts, an unpredicted syntax error was occurring. As a workaround the command to be run is now written into a file which is then run.

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The "--f1r2-tar-gz" input is used in FilterMutectCalls (check: https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest).
The "---germline-resource" input was already available in gatk 4.1.0.0.

Without this input attribute using the PoN would not be possible.