GenPipes 4.3.2 Release Notes

What’s new?

This release is mainly a bug-fix release.

• Tumor Pair: Fixed ‘sambamba sort’ crashing issues encountered with some tumor pair samples.

• DNA Sequencing Pipeline (SV): Several bugs were fixed in this pipeline after we identified and repaired some weakness spots in our testing suite.

• RNA Sequencing Pipeline: Now allows for batch effect correction (with DESeq2).

• The “resources <https://bitbucket.org/mugqic/genpipes/src/master/resources/>” folder is no more part of the GenPipes 4.3.2 release but remains accessible in our repository.

  Please note that as a consequence, the Homo sapiens configuration files formerly in resources/genomes/config folder have been moved to pipelines/common ini folder.

• Besides the above mentioned updates, this release includes lots of code clean ups and linting changes.

Quick! Where can I find it? I can’t wait!

• The latest release for GenPipes version 4.3.2 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.2.tar.gz

• The module mugqic/genpipes/4.3.2 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!