Fix: #240 v4.4.4 RN update

docs/VERSION

@@ -1 +1 @@
-4.4.3
+4.4.4

docs/source/development/release_notes.rst

@@ -9,6 +9,7 @@ The current release of GenPipes is |genpipes_version|.
 
 Following links point to the recent GenPipes release notes.
 
+* :ref:`GenPipes 4.4.4<docs_gp_relnote_4_4_4>` released on September 11, 2023
 * :ref:`GenPipes 4.4.3<docs_gp_relnote_4_4_3>` released on August 24, 2023
 * :ref:`GenPipes 4.4.2<docs_gp_relnote_4_4_2>` released on June 22, 2023
 * :ref:`GenPipes 4.4.1<docs_gp_relnote_4_4_1>` released on Mar 14, 2023

docs/source/development/relnotes/gp_4_4_3.rst

@@ -1,6 +1,6 @@
 :orphan:
 
-.. _docs_gp_relnote_4_4_2:
+.. _docs_gp_relnote_4_4_3:
 
 .. spelling::
 
@@ -18,13 +18,13 @@ This is a bug-fix minor release with the following updates to the pipelines:
 
 * `CoVSeq Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/covseq/>`_` :
       - Fixed a bug that was affecting the prepare_table/prepare_report steps when two similarly named samples were in the same run
-* `MethylSeq <https://bitbucket.org/mugqic/genpipes/src/4.4.2/pipelines/methylseq/>`_:
+* `MethylSeq <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/methylseq/>`_:
       - Updated version of bis-SNP to 1.0.0
       - Improved multiqc report
-* `Tumor Pair <https://bitbucket.org/mugqic/genpipes/src/4.4.2/pipelines/tumor_pair/>`_:
+* `Tumor Pair <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/tumor_pair/>`_:
       - Improved documentation
       - Added md5 for GATK recalibration output BAM
-* `RNASeq Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.2/pipelines/rnaseq/>`_:
+* `RNASeq Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/rnaseq/>`_:
       - Fixed issue where star_fusion would not re-run properly
       - Small fixes to dependencies to avoid unnecessary restarts
 * `RNASeq Light Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.3/pipelines/rnaseq_light/>`_ :

docs/source/development/relnotes/gp_4_4_44.rst

@@ -0,0 +1,56 @@
+:orphan:
+
+.. _docs_gp_relnote_4_4_4:
+
+.. spelling::
+
+     sed
+     sambamba
+     genpipes
+
+GenPipes 4.4.4 Release Notes
+============================
+
+What's new? 
+-----------
+
+This is a bug-fix minor release with the following updates to the pipelines:
+
+* `Tumor Pair <https://bitbucket.org/mugqic/genpipes/src/4.4.4/pipelines/tumor_pair/>`_:
+      - Fixed a bug in the interval_list creation step when using an exome BED file for the ensemble protocol
+      - Improved dependencies
+* `RNASeq Light Pipeline <https://bitbucket.org/mugqic/genpipes/src/4.4.4/pipelines/rnaseq_light/>`_ :
+      - Updated version of Kallisto to 0.50.0
+      - Renamed kallisto indexes to be more informative with regards to version used
+
+      .. warning:: "Update custom .ini file"
+
+            The indexes renaming on kallisto may prevent older versions of the GenPipes config file to not locate the proper index file. 
+
+            Care should be taken to update custom ini files, especially if using older versions of GenPipes, with something other than default versions of kallisto. 
+
+
+
+
+Quick! Where can I find it? I can't wait! 
+------------------------------------------
+
+* The latest release for GenPipes version 4.4.4 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.4.4.tar.gz
+
+* The module mugqic/genpipes/4.4.4 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!