Nextflow

- Added support for AWS S3 storage
- Added support for ClusterK Cirrus cloud scheduler
- Added multiple debugging level in command scripts by using `NXF_DEBUG` variable
- Added ability to disable docker kill command
- Added explicit `entrypoint` definition in docker run command
- Added `uge` executor as alias of SgeExecutor class
- Added `-D` JVM properties command line option
- Added `.command.log` to grid executors
- Separated `stdout` and `stderr` outputs
- Refactored DRMAA executor to a separate sub-project
- Refactored application packaging based on Capsule modes
- Refactored application installer downloading dependencies at runtime
- Optimised file attributes access usage
- Increased log and trace files rolling max index to 9
- Print revision and commit ID on pipeline startup
- Improved handling of docker cpuset for `crg` executor
- Improved TraceFileObserver to flush written content
- Improved `info <pipeline>` command with `-d` option that shows git revision commit IDs
- Fixed issue 39 - Per process containers not working with -with-docker option
- Upgraded Groovy runtime to version 2.3.11
- Upgraded Logback library to version 1.1.3

- Fixed regression preventing jobs cleanup when nextflow process is killed
- Fixed issue when command line flag has not value making it to consume following option
- Added `uge` executor as alias of SgeExecutor class
- Improved log messages
- Upgraded Spock testing library to version 1.0

- Added suspended job status handling to SLURM executor -- Issue 36
- Added `print` and `println` operators plus tests and updated docs
- Fixed issue on `view` operator when specifying a closure
- Fixed Docker image resource request in CRG executor
- Fixed typo in documentation
- Improved task hash key generation and task variables handling
- Compute `baseDir` and `workDir` as string values when creating task unique hash
- Improved `sum` operator to allows it to handle lists with varying size
- Upgrading Groovy runtime to version 2.3.10

- Added support for `module` and `container` fields in execution trace log
- Fixed a small inconsistency on polling monitor queue size for local executor when using single core or two-cores cpu
- Enhanced process key generation including global variables referenced in the process scope
- Enhanced `sum` operator and added `mean` operator

- Fixed issue on some SGE implementation where `-terse` directive in job script is not working
- Downgrade Capsule to 0.9.0 due to an issue in version 0.10.0 - https://github.com/puniverse/capsule/issues/56

- Fixed NoSuchMethodException issue on Java 1.7.0_01 due to missing private constructor
- Fixed logging issue on Nextflow console
- Fixed issue `view` operator which hung when used on a dataflow variable
- Upgrade SLF4J to version 1.7.10
- Upgrade Capsule to version 0.10.0
- Removed dependency on jsr166y module
- Removed `synchronized` declaration on Session cleanUp method