Release of GenPipes 5.0.2

[Mareike Janiak]

A new release of GenPipes, 5.0.2 is now available.

 

What's new? 

==========

This is a bug-fix minor release : 

* Core:

     - genpipes can now be loaded with 'module load genpipes/5.0.2' in addition to 'module load mugqic/genpipes/5.0.2'

     - for users on abacus, the flag 'force_mem_per_cpu' is now set by default

     - bug fix in the chunk_genpipes.sh script

     - the support script csvToreadset.R is once again available

* AmpliconSeq

     - fixed grep call that was matching multiple samples in some cases

* ChipSeq

     - reintroduced SampleMetrics.tsv report that was removed in 5.0.1, it now includes additional metrics (number of peaks, frip)

     - fixed missing input samples in IHEC metrics report

     - MultiQC report improved - the samtools flagstat metrics included now reflect the pre-filtered alignment stats, giving a better idea of total vs. mapped reads

* DNASeq

     - bumped version of pcgr to 2.1.2

* RNASeq

     - bumped version of pcgr to 2.1.2

     - improved handling of custom gtf files when using non-model genomes

Where to find it?

============ 

* The source code for this version is in bitbucket : 

https://bitbucket.org/mugqic/genpipes/downloads/genpipes-5.0.2.tar.gz

* GenPipes is now distributed as a package via pypi:

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

* The module genpipes/5.0.2 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)