diff --git a/build.gradle.kts b/build.gradle.kts index 4a250d5e0..40da43464 100644 --- a/build.gradle.kts +++ b/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 { diff --git a/changelogs/v4.1.2.md b/changelogs/v4.1.2.md index 518da1922..3710714d7 100644 --- a/changelogs/v4.1.2.md +++ b/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 `` to `` 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 `` to `` 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