Release of GenPipes 4.4.0

[edouard.henrion]

A new release of the GenPipes, 4.4.0 is now available.

 

What's new? 

==========

This is a medium release :

* Tumor Pair : revamping of the ‘sv’ protocol
      - GRIDSS to detect genomics rearrangements and call structural variations,

      - PURPLE adds information from the SV call to improve purity and ploidy estimates,

      - Linx for structural variants annotation.

* RNASeq :

      - addition of the ‘variants’ protocol :

small variant calling using gatk best practices
      - addition of the ‘cancer’ protocol :

small variant calling using gatk best practices,

fusion calling with STAR-Fusion, Arriba and annoFuse,

CPSR/PCGR reporting
      - deprecation of the ‘cufflinks’ protocol

* RNASeq Light :

      - calls to `kallisto quant` are now aggregated by sample instead of by readset

* Overall strengthening of the job dependencies

 

Where to find it?

============ 

* The source code for this version is in bitbucket : 

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, Graham, Cedar and Narval Compute Canada clusters.

 

* The source code is in bitbucket :

https://bitbucket.org/mugqic/genpipes

 

* For more 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