GenPipes 4.0.0 Release Notes

What’s new?

• Major Update:

  • GenPipes now supports Python3 and is NOT backwards compatible with GenPipes versions before this release regarding Python3 support.

    Python3 version(s) supported: 3.9.1

  • A new GenPipes Pipeline epiQC has now been added! Refer to Pipeline Reference Guide for details.

  • GenPipes offers new helper utilities that make submitting jobs and monitoring them much easier with better scheduler integration. These utilities are:

    • chunk_genpipes.sh

    • monitor.sh

    For detailed usage, refer to GenPipes documentation for: Submitting GenPipes Jobs.

• Other Updates:

  • RNASeq Denovo assembly now supports two protocols: Trinity and Seq2Fun. For details, refer to RNASeq DeNovo Assembly documentation.

  • Tumor Pair Pipeline documentation is not yet current, we are working on it.

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

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.0.0.tar.gz

• The module mugqic/genpipes/4.0.0 is installed on Abacus (MGC), Béluga, Graham and Cedar 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!