GenPipes 4.1.0 Release Notes

What’s new?

• Major Updates:

  • New pipeline introduced : nanopore_covseq is designed to help run the ARTIC Bioinformatics SARS-CoV-2 corona virus protocol. Both V4 and V4.1 of the protocol are supported. It requires additional .ini file, read Nanopore CoVSeQ Pipeline Documentation for usage details and more.

• Other Updates:

  • CoVSeQ Pipeline handles both Illumina and Nanopore read files:

    • Added compatibility to ARTIC primer versions 4 and 4.1

    • ncov-tools version 1.8 is now supported by this pipeline for better quality control using latest ARTIC v4 primer schemes.

  • ChIPSeq : added differential binding to the atacseq protocol

  • GenPipes helper utility introduced in GenPipes V4.0.0 called `monitor.sh` has been renamed to `submit_genpipes` in this release.

    For detailed usage of submit_genpipes utility, refer to GenPipes documentation for: Submitting GenPipes Jobs.

  • Tumor Pair Pipeline documentation is partially updated, we are working on completing the pipeline schema and workflow diagrams.

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

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.1.0.tar.gz

• The module mugqic/genpipes/4.1.0 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!