Nextflow

- Added support for file templates in process definition
- Added process `when` guard for conditional execution
- Added process `shell` block that allows both BASH and Groovy variables in the same script block
- Added support for includes in configuration files
- Added support for profiles in configuration files
- Added channel operator `set { }`
- Added channel operator `into { }`
- Added channel operator `tap { }`
- Added channel method `close()`
- Added channel factory `value()`
- Added `fixOwnership` docker config option
- Added `unstageStrategy` process config option
- Added minlog-slf4j kryo logging redirection
- Added `ext` directive for user defined configuration properties
- Added support for multi-indices grouping key to `groupTuple` operator
- Fixed issue that caused task attribute to be lost when resuming execution
- Fixed pipeline hangs when `map` operator is applied to a dataflow variables - Issue 44
- Fixed pipeline hangs when `into` operator is applied to a dataflow variable
- Improved dynamic code compilation with `Grengine` module
- Increased default queue size to 100 tasks when using a grid executor
- Refactored `Session` to remove dependency with `CmdRun` object Added ability to set `workDir` in the config file
- New implicit lazy Gstring in process parameter and directive definitions
- Changed file unstage strategy using `cp` command instead of `rsync` I
- Removed `workDir` variable from config file
- Updated JGit to version 3.7.1
- Updated Slf4j to version 1.7.12

- Fixed issue 44 - Pipeline hangs when `map` operator is applied to a dataflow variable

- Added html processes execution time report
- Added support for Docker executable containers - Feature 33
- Added support for missing number types to CacheHelper
- Added warning message when using a deprecated input/output shared parameter
- Fixed issue causing process hangs when stdout+stderr is bigger than 64K when using local executor
- Fixed process stdout/stderr synchronisation issue
- Fixed race condition when accessing `processor` attribute - Issue 41
- Fixed race condition on processes registration/termination - See issue 43
- Fixed `echo` synchronisation strategy when writing to stdout
- Use a fixed thread pool for tasks execution and keep it separated from Gpars thread pool
- Do not set Gpars thread pool size along with nextflow pool size
- Improved resolution to tenths of a second when converting a `Duration` to string
- Removed unnecessary local scope map argument from `getTaskGlobalVars` method
- Read trace file w/o checking existence in order to reduce round-trip on remote storage
- Workaround for Groovy compiler issue GROOVY-7409

- Fixed issue when staging file when using a non local pipeline workdir
- Fixed invalid values in the trace file returned by `awk`
- Removed unnecessary `S3Path` serialiser registration on DnaNexus executor initialisation
- Updated S3 file system client to version 0.2.8g

- Handle staging in the local process directory of files on remote/foreign file systems
- Fixed issue in resources stats tracing script -- awk uses scientific notation for numbers instead of decimal format.
- Fixed external links to Groovy docs
- Fixed issue 40 -- Cannot find java binary on Mac OSX
- Fixed missing `DynamicParameter` in usage string
- Fixed docker run `—-cpuset` command line option when using `crg` executor

- Fixed IllegalStateException when executing a script in Nextflow console