:orphan:

.. _docs_gp_relnote_5_0_2:

.. spelling:word-list::

     genpipes
     rnammer
     gtf

GenPipes 5.0.2 Release Notes
============================

What's new? 
-----------

This is a bug-fix minor release : 

* Core updates:
  
  - 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 fixed in the `chunk_genpipes.sh` script
  - Support script `csvToreadset.R` is now available for use
 
* `AmpliconSeq <https://genpipes.readthedocs.io/en/genpipes-v5.0.2/user_guide/pipelines/gp_ampliconseq.html>`_
  
  - `grep` call that was matching multiple samples in some cases is now fixed
* `ChipSeq <https://genpipes.readthedocs.io/en/genpipes-v5.0.2/user_guide/pipelines/gp_chipseq.html>`_
* 
  - Re-introduced `SampleMetrics.tsv` report that was removed in v5.0.1, 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
  
* `DNA Sequencing Pipeline <https://bitbucket.org/mugqic/genpipes/src/5.0.2/pipelines/dnaseq/>`_
  
  - bumped version of `pcgr` to 2.1.2
  
* `RNA Sequencing Pipeline <https://bitbucket.org/mugqic/genpipes/src/5.0.2/pipelines/rnaseq/>`_
  
  - Bumped version of `pcgr` to 2.1.2
  - Improved handling of custom gtf files when using non-model genomes

Quick! Where can I find it? I can't wait! 
------------------------------------------
 
* The latest release for GenPipes version 5.0.2 tarball is in: 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/](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 latest GenPipes documentation, please refer to: https://genpipes.readthedocs.io/

Where is the detailed ChangeLog? 
================================= 

A ChangeLog (`CHANGELOG.md <https://bitbucket.org/mugqic/genpipes/src/master/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 <https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh>`_ written by the author of the Ray assembler: Sébastien Boisvert, which lists the commits by tag and author. 

We look forward to your feedback!