Added
- New command-line interface (CLI) based on sub-commands
- New subcommand (`looper summarize`) replacing the `summarizePipelineStats.R` script
- New subcommand (`looper check`) replacing the `flagCheck.sh` script
- New command (`looper destroy`) to remove all output of a project
- New command (`looper clean`) to remove intermediate files of a project flagged for deletion
- Support for portable and pipeline-independent allocation of computing resources with Looperenv.
Changed
- Removed requirement to have `pipelines` repository installed in order to extend base Sample objects
- Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further)
- Improved serialization of Sample objects