Removed "pipefail" from command sections TALON and TranscriptClean

Removed "pipefail" from command sections TALON and TranscriptClean because no pipes are used. (Based on minimap2.wdl pull request)

BIOWDL-258: Add WDL task for Minimap2

 BIOWDL-260: Add WDL task for TALON

BIOWDL-259:  Add WDL task for TranscriptClean 

Combined outputDirPath and outputPrefix to outputPrefix and changed optional inputs with a default value to non optional

Update fastqsplitter

Update default memory values and CombineVariants to run in Shark

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.

Simplify cutadapt.