Merge pull request #1570 from milaboratory/fix-report-name

fix file names for analyze

build.gradle.kts

@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.6.0-78-fix-allele-naming"
+val mixcrAlgoVersion = "4.6.0-81-fix-report-name"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)

changelogs/v4.6.1.md

@@ -2,7 +2,7 @@
 
 - Consensus assembly in `assemble` now is performed separately for each chain. This allows to prevent effects from
   different expression levels on the consensus assembly algorithm. This change is specifically important for single-cell
-  presets with cell-level assembly (most of the MiXCR presets for single-cell data). 
+  presets with cell-level assembly (most of the MiXCR presets for single-cell data).
 
 ## 🛠️ Minor improvements & fixes
 
@@ -30,8 +30,10 @@
 - Fixed `IllegalStateException` on removing unnecessary genes on `findAlleles`
 - Added `--dont-remove-unused-genes` option to `findAlleles` command
 - Adjustment consensus assembly (in `assemble`) parameters for single cell presets
-- Command `groupClones` was renamed to `assembleCells`. Old name is working, but it's hidden from help
+- Command `groupClones` was renamed to `assembleCells`. Old name is working, but it's hidden from help. Also report and
+  output file names in `analyze` step were renamed accordingly.
 - Fixed calculation of germline for `VCDR3Part` and `JCDR3Part` in case of indels inside CDR3
 
 ## New Presets
- - Added preset 'takara-mouse-rna-bcr-umi-smarseq' for new Takara SMART-Seq Mouse BCR (with UMIs) kit
+
+- Added preset 'takara-mouse-rna-bcr-umi-smarseq' for new Takara SMART-Seq Mouse BCR (with UMIs) kit

itests/case-base_single_cell.sh

@@ -33,12 +33,12 @@ mixcr analyze --verbose 10x-sc-xcr-vdj \
 
 assert "cat base_single_cell.vdjcontigs.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "6"
 
-assert "mixcr exportClones --no-header base_single_cell.vdjcontigs.grouped.clns | wc -l" "6"
-assert "mixcr exportClones --no-header --split-by-tags Cell base_single_cell.vdjcontigs.grouped.clns | wc -l" "6"
-assert "mixcr exportClones --no-header --split-by-tags Molecule base_single_cell.vdjcontigs.grouped.clns | wc -l" "59"
-assert "mixcr exportClones --no-header -tags Molecule base_single_cell.vdjcontigs.grouped.clns | wc -l" "59"
-assert "mixcr exportClones --no-header --drop-default-fields -cellGroup base_single_cell.vdjcontigs.grouped.clns | sort | uniq | wc -l" "3"
-
-assert "mixcr exportClones --no-header --add-export-clone-grouping tag:CELL --drop-default-fields -readFraction base_single_cell.vdjcontigs.grouped.clns | jq -s add" "3"
-assert "mixcr exportClones --no-header --add-export-clone-grouping tag:CELL --drop-default-fields -uniqueTagFraction Molecule base_single_cell.vdjcontigs.grouped.clns | jq -s add" "3"
+assert "mixcr exportClones --no-header base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "6"
+assert "mixcr exportClones --no-header --split-by-tags Cell base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "6"
+assert "mixcr exportClones --no-header --split-by-tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "59"
+assert "mixcr exportClones --no-header -tags Molecule base_single_cell.vdjcontigs.assembledCells.clns | wc -l" "59"
+assert "mixcr exportClones --no-header --drop-default-fields -cellGroup base_single_cell.vdjcontigs.assembledCells.clns | sort | uniq | wc -l" "3"
+
+assert "mixcr exportClones --no-header --add-export-clone-grouping tag:CELL --drop-default-fields -readFraction base_single_cell.vdjcontigs.assembledCells.clns | jq -s add" "3"
+assert "mixcr exportClones --no-header --add-export-clone-grouping tag:CELL --drop-default-fields -uniqueTagFraction Molecule base_single_cell.vdjcontigs.assembledCells.clns | jq -s add" "3"