Release of GenPipes 5.0.1

[Mareike Janiak]

A new release of GenPipes, 5.0.1 is now available.

 

What's new? 

==========

This is a major release : 

   - GenPipes 5.0 distribution is now based on Python packaging and can be installed via pip.

   - The command syntax to run GenPipes pipelines has changed. Pipelines are now invoked with `genpipes <pipeline> -h` instead of `<pipeline>.py -h`.

    - Genome build GRCh38 (human) is now the default reference genome for all pipelines, but other versions or species can be selected via config files, as before.

    - Markdown style reports have been deprecated for all pipelines in v5.0.0 and have been replaced entirely with MultiQC reports.

    - When using GenPipes as a module on the Digital Research Alliance clusters, such as beluga, a new variable $GENPIPES_INIS is introduced for streamlining access to the config files in genpipes commands:

          $MUGQIC_PIPELINES_HOME/pipelines/<pipeline>/<pipeline>.base.ini

is now $GENPIPES_INIS/<pipeline>/<pipeline>.base.ini

* EpiQC, HiC-Seq, and AmpliconSeq QIIME

    - These protocols have been deprecated and are not available in the current version. Please use GenPipes v4.6.1 to run these pipelines/protocols.

* TumorPair and DNASeq-High Coverage

     - These pipelines have been merged into the DNASeq pipeline, where they are available as protocols. 

* AmpliconSeq

     - The dada2 protocol is now the default and is the only available protocol for this pipeline.

     - MultiQC reporting has been added.

* DNASeq

     - The DNASeq pipeline has been completely reworked and now includes protocols for germline, germline high coverage, and somatic analyses, for both exome and wgs experiments.

     - For further details about the changes to DNASeq, please refer to the bitbucket repository or the GenPipes documentation. 

* RNASeq-denovo

     - The trinity protocol has been updated to support Trinity v2.15.1

     - rnammer has been replaced with infernal, in accordance with changes made in Trinotate v4.0.2

     - MultiQC reporting has been added.

* MethylSeq

     - A new protocol called gembs is now available, which uses GemBS for mapping and methylation calling.

Where to find it?

============ 

* The source code for this version is in bitbucket : 

https://bitbucket.org/mugqic/genpipes/downloads/genpipes-5.0.1.tar.gz

* GenPipes is now distributed as a package via pypi:

https://pypi.org/project/c3g-genpipes/

* The module mugqic/genpipes/5.0.1 is installed on Abacus (MGC), Béluga, Graham, Cedar and Narval Alliance 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 

--

Mareike Janiak

Bioinformatics Analyst - Technical Development

Canadian Centre for Computational Genomics (C3G)