Commit 1f1315c5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added more to the release notes

parent f6116a57
......@@ -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/
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* Added metagenomics pipeline: [Gears](../pipelines/
* 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
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