Release notes Biopet version 0.5.0

General Code changes

  • Upgrade to Queue 3.4, with this also the htsjdk library to 1.132
  • Our QC and Mapping pipeline now use piping for the most used aligners and QC tools
    • Reducing I/O over the network
    • Reducing the disk usage (storage) and run time
  • Added version command for Star
  • Seperation of the biopet-framework into: Core, Extensions, Tools and Utils
  • Optimized unit testing
  • Unit test coverage on Tools increased
  • Workaround: Added R-script files of Picard to biopet to fix picard jobs (files are not packaged in maven dependency)
  • Added external example for developers


  • Retries of pipeline and tools is now enabled by default
  • Improvements in the reporting framework, allowing custom reporting elements for specific pipelines.
  • Fixed reports when metrics of Flexiprep is skipped
  • Added metagenomics pipeline: Gears
  • Added single sample variantcalling with bcftools
  • Added ET + key support for GATK job invocation, disable phone-home feature when key is supplied
  • 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
  • Shiva: fixed a lot of small bugs when developing integration tests
  • Shiva: Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder
  • Gentrap: Improved error handling on missing annotation files

Infrastructure changes

  • Development environment within the LUMC now get tested with Jenkins
    • Added integration tests Flexiprep
    • Added integration tests Gears
    • Added integration tests Mapping
    • Added integration tests Shiva
    • Added integration tests Toucan