Nextflow

- Fixed Command line params do not override params defined in the nextflow.config file 202

- Fixed Ability to customize job name submitted to the scheduler 140
- Fixed Duplicate output error when no channel specified 182
- Fixed File paths containing a timestamp are parsed as a Duration object 185
- Fixed ClosedByInterruptException is thrown randomly 188
- Fixed Pipeline hangs when `Channel.from` argument is an empty list 189
- Fixed Handle customised sbatch returning the jobid by itself 190
- Fixed LocalExecutor can randomly hang with no running task 191
- Fixed Missing flag in SLURM `squeue` call 193
- Fixed Process script declaring a regexp expression results in a IllegalAccessException 199
- Merged Silence mkdir error if NXF_HOME not writable 187
- Refactored ParallelTaskProcessor and TaskProcessor classes to a single class
- Added `ST` and `BF` queue statuses to SLURM executor
- Improved logging information
- Upgrade to Gradle 2.14

- Fixed Directives do not accept a negative numeric value 180
- Fixed Dynamic errorStrategy is not evaluated correctly 183
- Fixed Pipeline hangs when error strategy is used and an upstream process fail
- Added environment to ContainerBuilder and implement environment export for Shifter containers
- Updated Groovy runtime to version 2.4.7

- Added fromFilePairs channel factory method
- Added `finish` error strategy 158
- Added ability to change the name and the save path of published files 178
- Added a syntax validation check for process blocks keywords 177
- Fixed It's not possible to specify environment modules w/o a version number 174
- Fixed Local process kill signal is not propagated to children processes 172
- Fixed scratchDir is overwritten by TMPDIR 171
- Removed deprecated `Channel.path` methods
- Ignore missing COUT and CERR variables

- Fixed Exception is thrown while reporting an invalid output declaration 170

- Fixed Local executor does not run an job when host cpus == 1 166