Nextflow

- Changed caching hash function to murmur3_128 to avoid cache collision
- Fixed issue on process termination when resuming pipeline execution

- Major executors refactoring
- Featuring new single-thread tasks scheduler
- New enhanced DSL syntax with extended semantic
- Switched file handling to new NIO.2 file system
- Introducing support for DNAnexus cloud platform
- Removed unnecessary library dependencies
- Slim self-contained executable package

- Extending semantic for method File.copyTo(source,target) so that when 'target' argument
is a directory, it copies the 'source' file to that folder, with the same name as the original file.
- Bug: Fixed a ClassCastEx exception when the 'bin' folder is added to the PATH
- Bug: Fixed an issue that raised an error "error=26 Text file busy" on some platforms (CentOS)

- Added optional parameters to 'chunkLines' and 'chunkFasta' methods
- Added '-lib' command line parameter specify external libraries (.jar files) or extension scripts
- Folder 'lib' in the launch directory is added by as default libraries path
- Added 'tempFile()' and 'tempDir()' methods to BaseScript class
- The 'bin' directory in the script folder is added to the task PATH environment by default
- Upgraded to Groovy 2.1.6
- Upgraded to Slf4j 1.7.5
- Upgraded to Logback 1.0.13

- New command line option '-log' to specify the application log file
- New command line options '-task.xxx' to task default parameters (overriding the ones in the configuration file)
- Fixed a bug which was preventing the caching mechanism to work properly
- Fixed synchronization issue caused by a miss-used CountDownLatch, replaced with a Phaser
- Fixed a bug by which cached tasks didn't print out any result when 'echo' was set
- Fixed a bug in the timezone handling in the build timestamp

- Added command line parameter 'echo' to enable default tasks output
- Fixed an issue on merge task, when it doesn't collect any data the execution is skipped