Update default memory values and CombineVariants to run in Shark

  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.