New features:
- Added 2 new analysis modes - alignment-only and transcript assembly
- Alignment-only mode is designed to output alignment files (in BAM format) for each samples
- Transcript assembly mode is designed for performing transcript assembly from input samples to create an updated reference annotation
- Added Python3 support to all analysis modes (including Quantification analysis mode) and made PySpark use Python3 by default
- Added support for using custom AMI when launching EMR cluster (require EMR release >= 5.7)
Note: The default directory for application have now been set to /app rather than /mnt/app in order to support custom AMI when launching EMR cluster