Nextflow

- 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

- Added afterScript/beforeScript directives
- Added tag directive to label task executions with a custom identifier
- Added dynamic directives evaluation
- Added support for dynamic input/output file names with closures
- Added `ifEmpty` operator
- Added `view` operator
- Added `remainder` optional parameter to `phase` operator
- Removed 'undef' directive
- Refactored grid executors so that jobs directives are added on top of script wrapper
- Renamed ContextMap to TaskContext
- Renamed TaskConfig to ProcessConfig
- Renamed LocalConfig to TaskConfig
- Print pid/hostname in the status log
- Upgraded to Groovy 2.3.9 and Slf4j 1.7.8

- Fixed issue in TextFileCollector empty condition that was creating an empty split file
when the split size was equals to the number or records
- Fixed bug that prevents a job is added to the polling queue when submit operation fails
- Added more strict checks on $JAVA_CMD executable and $JAVA_HOME folder
- Refactored 'sge' and 'crg' executors so that qsub directives are provided on top of job wrapper script
- Added BSC specific executor
- Upgraded to Groovy 2.3.8

- Added to splitters ability to save chunks to files
- Fixed a bug that prevented an error message to be reported when using a missing variable in the process script
- Improved info command showing local and remote branches
- Improved error report when failing to delete pipeline directory
- Removed gpars methods implicit imports
- Fixed unit for 'syscr' and 'syscw' fields in trace report
- Upgraded JGit library version to 3.5.2.201411120430-r

- Added 'groupTuple' operator
- Added NXF_WORK variable to define default scratch path
- Added Gzip un-compress ability to splitter operators
- Added 'limit' parameter to splitter operators
- Added 'meta' parameter to splitter operators
- Field 'walltime' has been renamed to 'realtime' in tracing file
- Fixed issue on 'collectFile' operator when no 'name' parameter is specified
- Removed dependency on Picard library
- Improved error reporting

- Fixed serialisation issue on pipeline resume
- Fixed issue on command line parameters with no arg (flag)
- Refactored class HubOptions to a trait