GenPipes release 4.3.0

[edouard.henrion]

A new release of the GenPipes, 4.3.0 is now available.

 

What's new? 

==========

* MethylSeq : addition of 2 new protocols based on Illumina Dragen Bio-IT platform, tested on Abacus (the McGill Genome Center HPC) and usable where a “Dragen” allocation is available.

`bismark` protocol (former default protocol) uses Bismark to perform the whole analysis : read alignment, de-duplication, methylation calls

`dragen` protocol uses Dragen to perform the whole analysis
`hybrid` protocol uses Dragen for fast read alignment, and uses Bismark for the other steps.

* DNASeq : unmapped reads are now extracted from the merged/sorted bam files. Then, after the base recalibration step, the unmapped reads are “re-injected” into the fastq. This ensures to keep the unmapped reads for potential further analysis. Without this process, the base recalibration may eventually remove the unmapped reads.

* Some bug fixes e.g CovSeq report repaired for cases with multiple readsets per sample
* Standardization of the ini files

 

Where to find it?

============ 

* This version tarball is in bitbucket : 

https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.0.tar.gz

 

* The module mugqic/genpipes/4.3.0 is installed on Abacus (MGC), Béluga, Graham, Cedar and Narval Compute Canada clusters.

 

* The source code is in bitbucket :

https://bitbucket.org/mugqic/genpipes

 

* For more documentation, please refer to :
https://genpipes.readthedocs.io/ (updates for v4.3.0 are coming soon)

 

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 

 

 

Regards,
Edouard