GenPipes 3.1.4 Release Notes

What’s new?

• Bugs and issues which were introduced in GenPipes 3.1.3 and causing pipeline crash have been addressed and corrected

• Latest version of mugqic_tools (v2.2.2) is now used per default by GenPipes

• Latest version of mugqic_R_packages (v1.0.6) is now used per default by GenPipes

• MethylSeq pipeline :

  • Differential methylation analysis with ‘methylkit’

• Improvements of the RNASeq pipeline :

  • StringTie protocol added and set as default protocol : faster than cufflinks

• Improvements of the RNASeq_llight pipeline :

  • Added a differential analysis step, using Sleuth

• New log_report.py released for job tracking on a SLURM scheduler

• Config files for Cedar, Mp2b clusters are now available for all the pipelines

• Drafts of config files for Beluga cluster are now also available

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

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-3.1.4.tar.gz

• If you have a Compute Canada CCDB user account, the module mugqic/genpipes/3.1.4 is installed on Abacus, Guillimin, Mammouth-Mp2b, Graham and Cedar clusters, and soon will be deployed on Beluga as well.

• The source code is in bitbucket: https://bitbucket.org/mugqic/genpipes