Skip to content

Commit

Permalink
Refs: #195 GenPipes v4.3.2 RN updated
Browse files Browse the repository at this point in the history
  • Loading branch information
shaloo committed Dec 10, 2022
1 parent 8ed2b6a commit 3ef5f15
Show file tree
Hide file tree
Showing 3 changed files with 53 additions and 1 deletion.
2 changes: 1 addition & 1 deletion docs/VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
4.3.1
4.3.2
1 change: 1 addition & 0 deletions docs/source/development/release_notes.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ The current release of GenPipes is |genpipes_version|.

Following links point to the recent GenPipes release notes.

* :ref:`GenPipes 4.3.2<docs_gp_relnote_4_3_2>` released on Dec 8, 2022
* :ref:`GenPipes 4.3.1<docs_gp_relnote_4_3_1>` released on Oct 4, 2022
* :ref:`GenPipes 4.3.0<docs_gp_relnote_4_3_0>` released on June 15, 2022
* :ref:`GenPipes 4.2.0<docs_gp_relnote_4_2_0>` released on June 1, 2022
Expand Down
51 changes: 51 additions & 0 deletions docs/source/development/relnotes/gp_4_3_2.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
:orphan:

.. _docs_gp_relnote_4_3_2:

.. spelling::

sambamba
genpipes

GenPipes 4.3.2 Release Notes
============================

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

This release is mainly a bug-fix release.

* `Tumor Pair <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_tumourpair.html>`_: Fixed 'sambamba sort' crashing issues encountered with some tumor pair samples.

* `DNA Sequencing Pipeline (SV) <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_dnaseq.html>`_: Several bugs were fixed in this pipeline after we identified and repaired some weakness spots in our testing suite.

* `RNA Sequencing Pipeline <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_rnaseq.html>`_: Now allows for batch effect correction (with DESeq2).

* The "`resources <https://bitbucket.org/mugqic/genpipes/src/master/resources/>`" folder is no more part of the GenPipes 4.3.2 release but remains accessible in our repository.

Please note that as a consequence, the ``Homo sapiens`` configuration files formerly in ``resources/genomes/config`` folder have been moved to ``pipelines/common ini`` folder.

* Besides the above mentioned updates, this release includes lots of code clean ups and linting changes.

Quick! Where can I find it? I can't wait!
------------------------------------------

* The latest release for GenPipes version 4.3.2 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.2.tar.gz

* The module mugqic/genpipes/4.3.2 is installed on Abacus (MGC), Béluga, Narval, Graham and Cedar Compute Canada 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 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!

0 comments on commit 3ef5f15

Please sign in to comment.