1. Command line to start Picard has changed. Use:
    * `java -jar picard.jar <tool> <parameters>` 
  instead of:
    * `java -jar <tool>.jar <parameters>`

 2. To skip writing files for unmapped reads (FASTQ when using !IlluminaBasecallsToFastq or SAM/BAM when using !IlluminaBasecallsToSam), leave out the line with 'N' mapping in the multiplex parameters file.

 3. GZIP compression level can now be set with COMPRESSION_LEVEL command line parameter. Accepted values are 1-9.