GenPipes 4.4.3 Release Notes

What’s new?

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

• CoVSeq Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/covseq/>`_ :

  • Fixed a bug that was affecting the prepare_table/prepare_report steps when two similarly named samples were in the same run

• MethylSeq:

  • Updated version of bis-SNP to 1.0.0

  • Improved multiqc report

• Tumor Pair:

  • Improved documentation

  • Added md5 for GATK recalibration output BAM

• RNASeq Pipeline:

  • Fixed issue where star_fusion would not re-run properly

  • Small fixes to dependencies to avoid unnecessary restarts

• RNASeq Light Pipeline :

  • Updated version of Kallisto to 0.48.0

• Nanopore Pipeline :

  • Added BAM check to minimap2_align step to avoid false exit 0

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

• The latest release for GenPipes version 4.4.3 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.4.3.tar.gz

• The module mugqic/genpipes/4.4.3 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!