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Mirrors
biopet.biopet
Commits
1f1315c5
Commit
1f1315c5
authored
Nov 11, 2015
by
Peter van 't Hof
Browse files
Added more to the release notes
parent
f6116a57
Changes
1
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docs/releasenotes/release_notes_0.5.0.md
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1f1315c5
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*
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
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