chore: migrating deps to release versions

chore: final fixes for 4.1.2 changelog

build.gradle.kts

@@ -98,11 +98,11 @@ repositories {
     }
 }
 
-val milibVersion = "2.1.0-6-master"
-val repseqioVersion = "1.5.0-2-master"
-val miplotsVersion = "1.1.0-2-master"
-val mitoolVersion = "1.3.0-9-main"
-val jacksonBomVersion = "2.14.0"
+val milibVersion = "2.2.0"
+val repseqioVersion = "1.6.0"
+val miplotsVersion = "1.2.0"
+val mitoolVersion = "1.4.0"
+val jacksonBomVersion = "2.14.1"
 val redberryPipeVersion = "1.3.0"
 
 dependencies {

changelogs/v4.1.2.md

@@ -1,30 +1,36 @@
 # Major changes
 
-- Command `findShmTrees` now can build trees from inputs with different tags.
+- Command `findShmTrees` now can build trees from inputs with different tags
 - Added `--impute-germline-on-export` and `--dont-impute-germline-on-export` to `exportAlignments` and `exportClones`
   commands
 
 # Minor improvements
 
 - Now, instead of specifying separately multiple tags of the same type (i.e. CELL1+CELL2+CELL3) in filters, one can use
-  convenient aliases (like `allTags:Cell`, `allTags:Molecule`). This also facilitates creation of more generic base
-  preset implementing common single-cell and UMI filtering strategies.
-- Command line interface improvements
-- Migrate from `<tag_name>` to `<tag_type>` in export columns and `--split-by-tag` option
+  convenient aliases (like `allTags:Cell`, `allTags:Molecule`). This also facilitates creation of a more generic base
+  presets implementing common single-cell and UMI filtering strategies.
+- Several command line interface improvements
+- Migration from `<tag_name>` to `<tag_type>` semantics in export columns and `--split-by-tag` options
 
 # Fixes
 
 - fixes bug with `saveOriginalReads=true` on `align` leading to errors down the pipeline
 - `analyze` now correctly terminates on first error
-- correct progress reporting in `align` with multiple input files are use with file name expansion
+- correct progress reporting in `align` with multiple input files provided by file name expansion mechanism
 - fix `--only-observed` behaviour in `exportShmTreesWithNodes`
 - fix missing tile in heatmap
 - fix some cases of usage of `-O...`
 
 # Presets
-- Fixed issue with mouse presets from MiLab
+
+- Fixed issue with mouse presets from MiLaboratories
 - Fixed presets with whitelists
 - Fixed missing material type and species in several presets
 - Added template switch region trimming for RACE protocols
-- Added presets for: ThermoFisher oncomine kits,  ParseBio single cell protocol. iRepertoire kits, vergani-et-al-2017 publication, Cellecta air kit
+- Added presets for
+  - Thermo Fisher Oncomine kits
+  - ParseBio single-cell protocols
+  - iRepertoire kits
+  - Preset for protocol described in [Vergani *et al.* (2017)](https://doi.org/10.3389/fimmu.2017.01157)
+  - Cellecta AIR kit