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biopet.biopet
Commits
c6fd5e83
Commit
c6fd5e83
authored
Nov 12, 2015
by
Wai Yi Leung
Browse files
Update release notes and fix gears title
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docs/pipelines/gears.md
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c6fd5e83
#
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.
...
...
docs/releasenotes/release_notes_0.5.0.md
View file @
c6fd5e83
# 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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