GenPipes 4.4.0 Release Notes
What’s new?
This is a medium release with revamping of ‘sv’ protocol in the Tumor Pair pipeline and addition of a new protocol in the RNASeq pipeline.
Tumor Pair: ‘sv’ protocol updates
supports GRIDSS to detect genomics rearrangements and call structural variations
PURPLE adds information from the SV call to improve purity and ploidy estimates
supports Linx for structural variants annotation
RNA Sequencing Pipeline: - Newly added protocols:
‘variants’ protocol provides support for small variant calling using GATK best practices
‘cancer’ protocol provides support for:
small variant calling using GATK best practices
fusion calling with STAR-Fusion, Arriba and annoFuse
CPSR/PCGR reporting
Deprecated - the ‘cufflinks’ protocol is no longer supported
RNA Sequencing Light: - calls to kallisto quant are now aggregated by sample instead of by the readset
Overall, the job dependencies have been strengthened in GenPipes 4.4.0 release.
Quick! Where can I find it? I can’t wait!
The latest release for GenPipes version 4.4.0 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.4.0.tar.gz
The module mugqic/genpipes/4.4.0 is installed on Abacus (MGC), Béluga, Narval, Graham and Cedar Compute Canada clusters.
The source code is in bitbucket: https://bitbucket.org/mugqic/genpipes
For latest GenPipes documentation, please refer to: https://genpipes.readthedocs.io/
Where is the detailed ChangeLog?
A ChangeLog (CHANGELOG.md) is available in the archive as well as in the repository.
Since we use git, there are many ways to get the details in many formats. One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, which lists the commits by tag and author:
https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh
Enjoy our pipelines on the many clusters where they are installed!