GenPipes 4.4.4 Release Notes

What’s new?

This is a bug-fix minor release with the following updates to the pipelines:

• Tumor Pair:

  • Fixed a bug in the interval_list creation step when using an exome BED file for the ensemble protocol

  • Improved dependencies

• RNASeq Light Pipeline :

  • Updated version of Kallisto to 0.50.0

  • Renamed kallisto indexes to be more informative with regards to version used

  Warning

  Update custom .ini file

  The indexes renaming on kallisto may prevent older versions of the GenPipes config file to not locate the proper index file.

  Care should be taken to update custom ini files, especially if using older versions of GenPipes, with something other than default versions of kallisto.

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

• The latest release for GenPipes version 4.4.4 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.4.4.tar.gz

• The module mugqic/genpipes/4.4.4 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!