Added more to the release notes

docs/releasenotes/release_notes_0.5.0.md

@@ -3,4 +3,24 @@
 * Our QC and mapping pipeline now use piping for the most used aligners and QC tools
  * This decreases the disk usage and run time
 * Improvements in the reporting framework
-* Added metagenomics pipeline: [Gears](../pipelines/gears.md)
\ No newline at end of file
+* Added metagenomics pipeline: [Gears](../pipelines/gears.md)
+* Development envoirment within the LUMC now get tested with Jenkins
+ * Added integration tests Flexiprep
+ * Added integration tests Mapping
+ * Added integration tests Shiva
+ * Added integration tests Toucan
+* Added version command for Star
+* Added single sample variantcalling with bcftools
+* Splitting the Framework into: Core, Extensions, Tools and Utils
+* Fixed reports when Metrics of Flexiprep is skipped
+* Upgrade to Queue 3.4, with this also the htsjdk library to 1.132
+* Added key support for GATK jobs
+* Optimizing unit testing
+* Unit test coverage on Tools increased
+* Retry is now default enabled
+* Added more debug information in the `.log` directory when `-l debug` is enabled
+* Shiva: added support for GenotypeConcordance tool to check against a Golden Standard
+* Workaround: Added Rscript files of picard to biopet to fix picard jobs (files are not packaged in maven dependency)
+* Shiva: fixed a lot of small bugs when developing integration tests
+* Gentrap: Better error handeling on missing annotation files
+* Shiva: Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder