Nextflow

- Fixed PublishDir creates nested directory structures when a folder already exists 342
- Fixed NoSuchFileException is thrown when trace file path does not exist 334
- Fixed watchPath glob directory not working 335
- Fixed Channel.fromFilePairs does not handle properly multiple star wildcards 337
- Added executor for NQSII, queuing system used on NEC clusters.
- Added `relative` option to `fromPath` channel factory

- Fixed Process execution fails with not GNU version of sleep and date tools 321
- Fixed Pending processes are not cleaned up properly 322
- Fixed NPE is thrown when Singularity is enabled and a process uses no container 324
- Fixed Cached processes are not included in the timeline report 325
- Added MD5 digest file upload
- Updated docs

- Fixed Tuple array object deserialisation fails 317
- Use SLURM squeue —-noheader instead -h command line option to support not standard implementation 316
- Fixed Execution time is incorrect for the local executor 313

- Fixed Improve explanation of cache DB IOException 303
- Fixed Operator ifEmpty results in a error when applied to a dataflow variable 308
- Fixed Process execution fails when the work path contains a parenthesis character 310
- Fixed Installer script fails when current path contains a blank character 311
- Fixed Include SLURM partition when checking job status 312
- Allow the usage of `close` operator on unbounded dataflow variable

- Added new `combine` operator 298
- Added new `collect` operator 297
- Added new CLI option `-params-file` to load parameters from a json/yaml file 208
- Fixed SCM user name is not set accessing private repository 300
- Fixed Infer singleton process outputs from inputs declaration 301
- Fixed Use exit status 1 for all NF errors 304
- Fixed Invalid SGE job name as defined in `sge_types` 299
- Added `skip` parameter to collectFile operator 306
- Added experimental `fs` command
- Improved file staging error reports 295
- Upgraded Groovy to version 2.4.10

- Fixed Show a warning message when accessing undefined parameters 293
- Fixed Staging input files in a subfolder changes their names when they are symlinks 292
- Fixed NPE accessing foreign files
- Added column char to list of path escaped chars
- Fixed Boothook script fails on Ubuntu 16.04