@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.23.2 → 3.23.4

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.4 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 3.23.4
+
+### Patch Changes
+
+- 9c08972: Update RNA-seq preset
+
+## 3.23.3
+
+### Patch Changes
+
+- 81cea8f: Use topChains (intersection of best V/J/C hits) to enforce exclusivity when analyzing TRA or TRD
+
 ## 3.23.2
 
 ### Patch Changes

package/dist/tengo/lib/calculate-export-specs.lib.tengo

@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
+	isRnaSeqPreset := is_undefined(assemblingFeature)
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	clonotypeKeyArgs := undefined
 
 	if !is_undefined(assemblingFeature) {
-		clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
-		clonotypeKeyArgs = [
-			[ "-nFeature", assemblingFeature ],
-			[ "-vGene" ],
-			[ "-jGene" ]
-		]
+		if isRnaSeqPreset {
+			clonotypeKeyColumns = [
+				"nSeqFR1",
+				"nSeqCDR1",
+				"nSeqFR2",
+				"nSeqCDR2",
+				"nSeqFR3",
+				"nSeqCDR3",
+				"bestVGene",
+				"bestJGene"
+			]
+			clonotypeKeyArgs = [
+				[ "-nFeature", "FR1" ],
+				[ "-nFeature", "CDR1" ],
+				[ "-nFeature", "FR2" ],
+				[ "-nFeature", "CDR2" ],
+				[ "-nFeature", "FR3" ],
+				[ "-nFeature", "CDR3" ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		} else {
+			clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
+			clonotypeKeyArgs = [
+				[ "-nFeature", assemblingFeature ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		}
 		if splitByC {
 			clonotypeKeyColumns += ["bestCHit"]
 			clonotypeKeyArgs += [ [ "-cHit" ] ]

package/package.json

@@ -1,13 +1,13 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.23.2",
+  "version": "3.23.4",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.8.2",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-302-develop"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.17"
+    "@platforma-sdk/tengo-builder": "2.4.18"
   },
   "scripts": {
     "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",

package/src/calculate-export-specs.lib.tengo

@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
+	isRnaSeqPreset := is_undefined(assemblingFeature)
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	clonotypeKeyArgs := undefined
 
 	if !is_undefined(assemblingFeature) {
-		clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
-		clonotypeKeyArgs = [
-			[ "-nFeature", assemblingFeature ],
-			[ "-vGene" ],
-			[ "-jGene" ]
-		]
+		if isRnaSeqPreset {
+			clonotypeKeyColumns = [
+				"nSeqFR1",
+				"nSeqCDR1",
+				"nSeqFR2",
+				"nSeqCDR2",
+				"nSeqFR3",
+				"nSeqCDR3",
+				"bestVGene",
+				"bestJGene"
+			]
+			clonotypeKeyArgs = [
+				[ "-nFeature", "FR1" ],
+				[ "-nFeature", "CDR1" ],
+				[ "-nFeature", "FR2" ],
+				[ "-nFeature", "CDR2" ],
+				[ "-nFeature", "FR3" ],
+				[ "-nFeature", "CDR3" ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		} else {
+			clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
+			clonotypeKeyArgs = [
+				[ "-nFeature", assemblingFeature ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		}
 		if splitByC {
 			clonotypeKeyColumns += ["bestCHit"]
 			clonotypeKeyArgs += [ [ "-cHit" ] ]

package/src/mixcr-export.tpl.tengo

@@ -159,6 +159,15 @@ self.body(func(inputs) {
 		stopCodonTypes: stopCodonTypes,
 		stopCodonReplacements: stopCodonReplacements
 	})
+
+	// Filter for exclusive TRA/TRD chain assignment.
+	// MiXCR --chains filter is permissive (any V/J/C gene locus match),
+	// so clonotypes with shared TRDV genes pass both --chains TRA and --chains TRD.
+	// Use topChains (intersection of best V/J/C hits) to enforce exclusivity.
+	if chains == "TRA" || chains == "TRD" {
+		dfMain = dfMain.filter(pt.col("topChains").eq(chains))
+	}
+
 	dfMain.addColumns(
 		hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey")
 	)
@@ -177,7 +186,12 @@ self.body(func(inputs) {
 				arg("--split-by-tags").arg("Cell").
 				arg("-tags").arg("Cell")
 
-			for argGrp in (clonotypeKeyArgs + mainIsProductiveArgs + mainAbundanceColumnUnnormalizedArgs) {
+			scExportArgs := clonotypeKeyArgs + mainIsProductiveArgs + mainAbundanceColumnUnnormalizedArgs
+			// Add -topChains for TRA/TRD filtering (shared TRAD locus)
+			if chains == "TRA" || chains == "TRD" {
+				scExportArgs = scExportArgs + [[ "-topChains" ]]
+			}
+			for argGrp in scExportArgs {
 				for arg in argGrp {
 					mixcrCmdBuilder.arg(arg)
 				}
@@ -236,6 +250,12 @@ self.body(func(inputs) {
 			return allowed
 		}()
 		})
+
+		// Filter for exclusive TRA/TRD chain assignment (same as bulk path)
+		if chains == "TRA" || chains == "TRD" {
+			dfSingleCell = dfSingleCell.filter(pt.col("topChains").eq(chains))
+		}
+
 		dfSingleCell.addColumns(
 			hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey"),
 			hashCellKey ? hashKeyDerivationExpressionPt(cellTagColumns).alias("cellKey") : pt.col(cellTagColumns[0]).alias("cellKey")

package/src/test/columns.test.ts

@@ -111,6 +111,16 @@ const testCases: TestCase[] = [
       expect(config.columnsSpec.find((c: any) => c.column === 'readFraction')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'nSeqCDR3')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'aaSeqCDR3')).toBeDefined();
+      expect(config.clonotypeKeyColumns).toEqual([
+        'nSeqFR1',
+        'nSeqCDR1',
+        'nSeqFR2',
+        'nSeqCDR2',
+        'nSeqFR3',
+        'nSeqCDR3',
+        'bestVGene',
+        'bestJGene'
+      ]);
     }
   },
   {