GenPipes 4.3.1 Release Notes

What’s new?

This release is mainly a bug-fix release.

• Tumor Pair: Fix added to ensure that errors are detected for bwa_mem_sort_sam step.

• MethylSeq : Debugged and fixed filter_snp_cpg step.

• Nanopre CoVSeq: GPU_QUEUE bug is now fixed.

Other Updates:

• MethylSeq Pipeline: The differential expression analysis is now added back to the pipeline.

• All pipelines: The timestamp is added for every pipeline. Also the command used to run the pipeline is now added in the configuration trace file.

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

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.1.tar.gz

• The module mugqic/genpipes/4.3.1 is installed on Abacus (MGC), Béluga, Narval, 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!