GenPipes 4.4.2 Release Notes

What’s new?

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

• RNASeq Pipeline:

  • MultiQC step is added to aggregate results from the bioinformatics analyses across many samples into a single report. This step searches a given directory for analysis logs and compiles the results into an HTML report.

• MethylSeq:

  • Fixed small issue with ‘sambamba_merge_sam_files’ step by making options section in the config file as ‘not required’.

  • MultiQC step is added to aggregate results from the bioinformatics analyses across many samples into a single report. This step searches a given directory for analysis logs and compiles the results into an HTML report.

• ChipSeq:

  • Added option to filter BAMS for regions in the blacklist, prior to peak calling step.

• Tumor Pair:

  • Improved the MultiQC processing.

• DNASeq:

  • Fixed the ‘manta_sv_calls’ command by removing ‘sed’ call that removed ‘chr’ from the BED file.

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

• The latest release for GenPipes version 4.4.2 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.4.2.tar.gz

• The module mugqic/genpipes/4.4.2 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!