nextflow

• Fixed file close leaks
• Fixed DirectoryStream close leaks
• Enhanced process executor, supporting multiple executors in the same pipeline

• 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 DLS 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

11 Jul 2013

• Decoupled the processors logic by the execution strategy implementation
• Normalised script level arguments so that a blank char may be used in place of the equals char
• Added a new configuration option named 'clusterOptions' where specify grid native configuration parameters
• Added a new configuration option named 'scratch' which enable/disable usage of scratch temporary folder when using cluster executors
• Enhanced implementation of LSF executor