diff --git a/docs/VERSION b/docs/VERSION index f0f76fb..f15ec04 100644 --- a/docs/VERSION +++ b/docs/VERSION @@ -1 +1 @@ -4.4.3 \ No newline at end of file +4.4.4 \ No newline at end of file diff --git a/docs/source/development/release_notes.rst b/docs/source/development/release_notes.rst index eca4b7f..9cf5464 100644 --- a/docs/source/development/release_notes.rst +++ b/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` released on September 11, 2023 * :ref:`GenPipes 4.4.3` released on August 24, 2023 * :ref:`GenPipes 4.4.2` released on June 22, 2023 * :ref:`GenPipes 4.4.1` released on Mar 14, 2023 diff --git a/docs/source/development/relnotes/gp_4_4_3.rst b/docs/source/development/relnotes/gp_4_4_3.rst index 15ec07a..dc70208 100644 --- a/docs/source/development/relnotes/gp_4_4_3.rst +++ b/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 `_` : - Fixed a bug that was affecting the prepare_table/prepare_report steps when two similarly named samples were in the same run -* `MethylSeq `_: +* `MethylSeq `_: - Updated version of bis-SNP to 1.0.0 - Improved multiqc report -* `Tumor Pair `_: +* `Tumor Pair `_: - Improved documentation - Added md5 for GATK recalibration output BAM -* `RNASeq Pipeline `_: +* `RNASeq Pipeline `_: - Fixed issue where star_fusion would not re-run properly - Small fixes to dependencies to avoid unnecessary restarts * `RNASeq Light Pipeline `_ : diff --git a/docs/source/development/relnotes/gp_4_4_44.rst b/docs/source/development/relnotes/gp_4_4_44.rst new file mode 100644 index 0000000..dcc7295 --- /dev/null +++ b/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 `_: + - Fixed a bug in the interval_list creation step when using an exome BED file for the ensemble protocol + - Improved dependencies +* `RNASeq Light Pipeline `_ : + - 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 `_) 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!