Release v2.2.1

CHANGELOG.rst

@@ -8,14 +8,17 @@ Changelog
 .. that users understand how the changes affect the new version.
 
 **********
-v2.2.1-dev
+v2.2.1
 **********
 
 Breaking changes
 ================
 * The `bed_variant_call_regions` option has been removed, variants are now
   called for all genes present in the `gtf` file.
 * Add graphviz/`dot` as a dependency (developer only).
+* Please create a new HAMLET configuration file with `create-config.py` script.
+* To use the latest hotspot regions and artifact blacklist, please recreate the
+  HAMLET reference data.
 
 Novel module
 ============
@@ -25,14 +28,17 @@ Novel module
 
 Bugfixes
 ========
-* Fix a rare bug where different modules use the same multiqc file list.
-* Fix a bug with filtering VEP records that contain multiple population
+* Fix a rare bug where different modules use the same MultiQC file list.
+* Fix a bug with filtering VEP records that contain multiple population.
   frequency records for a single variant.
 
 Updates
 =======
 * Add ability to generate configurations for each module using the
   `utilities/create-config.py` script.
+* Update the hotspot regions reference file.
+* Update the blacklist of known artifacts.
+* Remove various superfluous plots from the MultiQC report.
 
 **********
 v2.1.3

common.smk

@@ -17,4 +17,4 @@ containers = {
 }
 
 # The version of HAMLET
-PIPELINE_VERSION = "v2.2.1-dev"
+PIPELINE_VERSION = "v2.2.1"

docs/source/conf.py

@@ -6,7 +6,7 @@
 copyright = '2018, LUMC'
 author = 'Wibowo Arindrarto, Redmar van den Berg, Xiaoyun Liu'
 
-release = "v2.2.1-dev"
+release = "v2.2.1"
 version = '.'.join(release.split('.')[0:2])
 
 # -- General configuration