Nextflow

- Fixed bug when composing SLURM 'squeue' command line which was containing
unnecessary quote characters thus invalidating the jobs status check mechanism

- Fixed bug while submitting a job to SLURM scheduler due to special characters in job name
- Fixed bug in TaskConfigtoBool() method
- Fixed bug resolving configuration file when pipeline script is a symlink
- Fixed bug while setting 'workDir' attribute on PBS job executor
- Improved error message when the name of a process is missing
- Removed TaskConfiggetMerge() method
- Updated method Channel.fromPath(String) so that it returns normalised absolute paths
- Updated Capsule to version 0.9.0 stable
- Fixed typos in documentation

- Added ability to 'run' implicitly a script when it's specified as the very first parameter (for backward compatibility)
- Added 'workDir' and 'baseDir' implicit variables in configuration files
- Fixed docker remove issue by executing as an external command
- Fixed an issue when finding the longest common path used by docker mounts
- Fixed issue 13 - Show a detailed error message when hitting GitHub rate limits

- Added DRMAA executor
- Added PBS/Torque executor
- Added processes execution report
- Added Extrae tracing support
- Added support for GitHub private repositories
- Added integration for BitBucket hosted repositories (Git vcs only)
- Added native integration AWS S3 file system
- Improved Docker support and configuration
- Improved GridGain cluster integration
- Removed Hazelcast integration
- Added Capsule based application packaging
- Added commands
view: that prints the content a pipeline repository
config: shows pipeline configuration
- Fixed issue 12 - Error resuming process with command defined on multiple lines

- Added GitHub/Git support. It allows one to pull and run pipelines published on a
remote GitHub repository
- Changed command line structure. Since this version it is organised in sub-commands.
The following sub-commands are available:
ls: list all downloaded pipelines;
run: launch a pipeline execution;
pull: download or update a pipeline hosted on GitHub;
info: show pipeline information;
drop: remote a locally stored pipeline;
clone: copy a pipeline to a directory specified;
history: list all pipeline runs;
help: show program help.
- Added 'baseDir' and 'workDir' script variables
- Removed Merge processor

- Upgraded to Groovy 2.3.6
- Added '-noverify' to JVM launcher options as workaround for Java bug JDK-8051012