update docs

lilab-bcb · Feb 3, 2024 · f3adf2b · f3adf2b
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diff --git a/docs/conf.py b/docs/conf.py
@@ -20,13 +20,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'Cumulus'
-copyright = '2022 Genentech, Inc. and the Broad Institute, Inc. All rights reserved.'
+copyright = '2024 Genentech, Inc. All rights reserved.'
 author = 'Yiming Yang, Joshua Gould and Bo Li'
 
 # The short X.Y version
-version = '2.3'
+version = '2.5'
 # The full version, including alpha/beta/rc tags
-release = '2.3.0'
+release = '2.5.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/index.rst b/docs/index.rst
@@ -5,7 +5,7 @@
 Release Highlights in Current Stable
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. include:: release_notes/version_2_4.rst
+.. include:: release_notes/version_2_5.rst
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -3,6 +3,11 @@ Release notes
 
 .. role:: small
 
+Version 2.5
+~~~~~~~~~~~~~~
+
+.. include:: release_notes/version_2_5.rst
+
 Version 2.4
 ~~~~~~~~~~~~~~
 

diff --git a/docs/release_notes/version_2_5.rst b/docs/release_notes/version_2_5.rst
@@ -0,0 +1,32 @@
+2.5.0 :small:`February 3, 2024`
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**Improvements:**
+
+* In Cellranger workflow:
+
+    * Add *multi_disk_space* input for specifying disk size used by Fixed RNA Profiling or 10x multiome jobs, which usually take large amount.
+
+* In Cellbender workflow:
+
+    * With ``0.3.0`` default Cell Bender version, users don't need to always specify *expected_cells* or *total_droplets_included* input.
+
+**Updates:**
+
+* In Cellranger workflow:
+
+    * Upgrade *cellranger_version*  default to ``7.2.0``.
+    * Upgrade *cumulus_feature_barcoding* version default to ``0.11.2``.
+    * Add GRCh38 VDJ v7.1.0 reference: ``GRCh38_vdj_v7.1.0``.
+
+* In Spaceranger workflow:
+
+    * Upgrade *spaceranger_version* default to ``2.1.1``.
+
+* In Demultiplexing workflow:
+
+    * Upgrade *souporcell_version* default to ``2.5``.
+
+* In Cellbender workflow:
+
+    * Upgrade *cellbender_version* default to ``0.3.0``.