Commit c6fd5e83 authored by Wai Yi Leung's avatar Wai Yi Leung
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Update release notes and fix gears title

parent 6f6a94c8
# Flexiprep
# Gears
## Introduction
Gears is a metagenomics pipeline. (``GE``nome ``A``nnotation of ``R``esidual ``S``equences). One can use this pipeline to identify contamination in sequencing runs on either raw FastQ files or BAM files.
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# Release notes Biopet version 0.5.0
* 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)
* 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
## 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
## Functionality
* 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](../pipelines/gears.md)
* 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 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
* 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
* Added external example for developers
* [Shiva](../pipelines/shiva.md): added support for `GenotypeConcordance` tool to check against a Golden Standard
* [Shiva](../pipelines/shiva.md): fixed a lot of small bugs when developing integration tests
* [Shiva](../pipelines/shiva.md): Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder
* [Gentrap](../pipelines/gentrap.md): 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
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