Major changes
- Changes to adopt Piper to running on the Milou cluster.
- All QScripts now get their settings from the setup xml.
- All the different DNA best practice scripts merged to a single QScript - making the process of running in much smoother, as well as simplifying future development considerably.
Minor changes
- Option to only run alignments in Haloplex workflow.
- Haloplex scripts will do a simple conversion of input files to run on b37 human reference instead of hg19.
- Adding some simple example scripts for demo purposes (to support the Piper workshop).
- ReportParser app added - a simple application to parse report files and extract the number of libraries sequenced and reads passed filter for a sample.
- Improvements to the documentation
- A lot of minor fixes.