GenPipes 3.5.0 Release Notes

What’s new?

• ChIPSeq pipeline updates:

  • Differential Analysis: A new step (Step 17) has been added to perform Differential Analysis using DiffBind Package.

  • Design File: In the previous release, design file was removed from Chip sequencing pipeline. It has been re-introduced with a brand new format. For details see ChIPSeq Pipeline Design File Format.

  • TSV File: The analysis generates a TSV file with differentially bound peaks and html reports for QC.

  • Workflow for ChIPSeq Pipeline has been updated to reflect addition of Differential Binding step.

• Added the “genpipes_file” parameter (optional) to allow users to specify the output file directly from the genpipes command line.

  For example:,

  Earlier, for the same purpose, users redirected the output to the command file before running the pipeline:

  chipseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.beluga.ini -r readset.chipseq.txt -d design.chipseq.txt -j slurm -t chipseq > chip_cmd.sh
  

  In the latest release, for any pipeline, users can use the following command and specify the command file name as an option:

  chipseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.beluga.ini -r readset.chipseq.txt -d design.chipseq.txt -j slurm -t chipseq --genpipes-file chip_cmd.sh
  

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

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-3.5.0.tar.gz

• The module mugqic/genpipes/3.5.0 is installed on Abacus (MGC), Béluga, Graham and Cedar clusters.

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

• For more 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!