@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.24.0 → 2.26.0

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@2.24.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.26.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > 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
 
+## 2.26.0
+
+### Minor Changes
+
+- 4d7746d: Cell Linker Column & SDK Upgrade
+
+## 2.25.0
+
+### Minor Changes
+
+- 427ffa6: Include junction lengths and total number of added nt
+
 ## 2.24.0
 
 ### Minor Changes

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

@@ -116,7 +116,7 @@ addSpec := func(columns, additionalSpec) {
 
 
 
-calculateExportSpecs := func(presetSpecForBack, blockId) {
+calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
@@ -125,6 +125,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	splitByC := ops.splitByC
 
 	isSingleCell := !is_undefined(cellTags) && len(cellTags) > 0
+	hashCellKey := isSingleCell && len(cellTags) == 1
 
 	assemblingFeatureInfo := assemblingFeatureInfo(assemblingFeature)
 	productiveFeature := assemblingFeatureInfo.productiveFeature
@@ -541,6 +542,52 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	}
 
 
+	junctionTypes := [ "VJ", "VD", "DJ" ]
+	for junctionType in junctionTypes {
+		feature := junctionType + "Junction"
+		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
+		
+		columnsSpecPerClonotypeNoAggregates += [ {
+			column: "nLength" + feature,
+			id: "n-length-" + text.to_lower(junctionType) + "-junction",
+			naRegex: naRegex,
+			allowNA: true,
+			spec: {
+				name: "pl7.app/vdj/sequenceLength",
+				valueType: "Int",
+				domain: {
+					"pl7.app/vdj/feature": feature,
+					"pl7.app/alphabet": "nucleotide"
+				},
+				annotations: a(orderP, false, {
+					"pl7.app/label": "Length of " + junctionType + " Junction nt"
+				})
+			}
+		} ]
+		exportArgs += [ [ "-nLength", feature ] ]
+		orderP -= 100
+	}
+	
+
+	columnsSpecPerClonotypeNoAggregates += [ {
+		column: "nLengthTotalAdded",
+		id: "n-length-total-added",
+		naRegex: "region_not_covered|no_d_gene",
+		allowNA: true,
+		spec: {
+			name: "pl7.app/vdj/sequenceLength",
+			valueType: "Int",
+			domain: {
+				"pl7.app/alphabet": "nucleotide"
+			},
+			annotations: a(orderP, false, {
+				"pl7.app/label": "Total number of added nt"
+			})
+		}
+	} ]
+	orderP -= 100
+
+
 
 	geneHitColumnVariants := [ {
 			name: "pl7.app/vdj/geneHitWithAllele",
@@ -765,9 +812,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
-	axesByClonotypeKey := undefined
-	axesByScClonotypeKey := undefined
+	axisByClonotypeKeyGen := undefined
+	axisByScClonotypeKeyGen := undefined
 	cellTagColumns := undefined
+	cellLinkerColumnSettingsGen := undefined
 
 	if !is_undefined(clonotypeKeyColumns) {
 
@@ -785,39 +833,16 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
-		axesByClonotypeKey = [ {
-			column: "clonotypeKey",
-			naRegex: "",
-			spec: {
-				name: "pl7.app/vdj/clonotypeKey",
-				type: "String",
-				domain: {
-					"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture)),
-					"pl7.app/vdj/clonotypingRunId": blockId
-				},
-				annotations: {
-					"pl7.app/label": "Clonotype ID",
-					"pl7.app/table/fontFamily": "monospace",
-					"pl7.app/table/visibility": "default",
-					"pl7.app/table/orderPriority": "110000",
-					"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
-				}
-			}
-		} ]
-
-		if isSingleCell {
-			cellTagColumns = slices.map(cellTags, func(cellTag) {
-				return "tagValue" + cellTag
-			})
-
-			axesByScClonotypeKey = [ {
-				column: "scClonotypeKey",
+		axisByClonotypeKeyGen = func(chain) {
+			return {
+				column: "clonotypeKey",
 				naRegex: "",
 				spec: {
-					name: "pl7.app/vdj/scClonotypeKey",
+					name: "pl7.app/vdj/clonotypeKey",
 					type: "String",
 					domain: {
-						"pl7.app/vdj/scClonotypeKey/structure": string(json.encode(keyStrincture)),
+						"pl7.app/vdj/chain": chain,
+						"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture)),
 						"pl7.app/vdj/clonotypingRunId": blockId
 					},
 					annotations: {
@@ -828,7 +853,69 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
 					}
 				}
-			} ]
+			}
+		}
+
+		if isSingleCell {
+			cellTagColumns = slices.map(cellTags, func(cellTag) {
+				return "tagValue" + cellTag
+			})
+
+			axisByScClonotypeKeyGen = func(receptor) {
+				return {
+					column: "scClonotypeKey",
+					naRegex: "",
+					spec: {
+						name: "pl7.app/vdj/scClonotypeKey",
+						type: "String",
+						domain: {
+							"pl7.app/vdj/receptor": receptor,
+							"pl7.app/vdj/scClonotypeKey/structure": string(json.encode(keyStrincture)),
+							"pl7.app/vdj/clonotypingRunId": blockId
+						},
+						annotations: {
+							"pl7.app/label": "Clonotype ID",
+							"pl7.app/table/fontFamily": "monospace",
+							"pl7.app/table/visibility": "default",
+							"pl7.app/table/orderPriority": "110000",
+							"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
+						}
+					}
+				}
+			}
+
+			cellLinkerColumnSettingsGen = func(receptor) {
+				return {
+					axes: [ {
+						column: "sampleId",
+						spec: sampleIdAxisSpec
+					}, {
+						column: "cellKey",
+						spec: {
+							name: "pl7.app/sc/cellId",
+							type: "String",
+							annotations: a(110000, true, {
+								"pl7.app/label": "Cell ID",
+								"pl7.app/table/fontFamily": "monospace",
+								"pl7.app/parents": string(json.encode([sampleIdAxisSpec.name]))
+							})
+						}
+					}, axisByScClonotypeKeyGen(receptor) ],
+					columns: [ {
+						column: "1",
+						spec: {
+							name: "pl7.app/sc/cellLinker",
+							valueType: "Int",
+							annotations: a(0, undefined, {
+								"pl7.app/label": "Cell Linker",
+								"pl7.app/isLinkerColumn": "true"
+							})
+						}
+					} ],
+					storageFormat: "Binary",
+					partitionKeyLength: 1
+				}
+			}
 
 
 
@@ -851,8 +938,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 		cellTagColumns: cellTagColumns,
 
-		axesByClonotypeKey: axesByClonotypeKey,
-		axesByScClonotypeKey: axesByScClonotypeKey,
+		axisByClonotypeKeyGen: axisByClonotypeKeyGen,
+		axisByScClonotypeKeyGen: axisByScClonotypeKeyGen,
 
 		columnsSpecPerSample: columnsSpecPerSample,
 		columnsSpecPerSampleSc: columnsSpecPerSampleSc,
@@ -870,7 +957,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		mainIsProductiveColumn: mainIsProductiveColumn,
 		mainIsProductiveArgs: mainIsProductiveArgs,
 
-		exportArgs: exportArgs
+		exportArgs: exportArgs,
+
+		hashCellKey: hashCellKey,
+		cellLinkerColumnSettingsGen: cellLinkerColumnSettingsGen
 	}
 }
 

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.24.0",
+  "version": "2.26.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.10.0",
+    "@platforma-sdk/workflow-tengo": "^4.14.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-190-develop"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.1.12",
-    "@platforma-sdk/test": "^1.39.21",
+    "@platforma-sdk/tengo-builder": "^2.1.13",
+    "@platforma-sdk/test": "^1.41.16",
     "vitest": "~2.1.9",
     "typescript": "~5.5.4"
   },

package/src/aggregate-by-clonotype-key.tpl.tengo

@@ -75,7 +75,7 @@ self.body(func(inputs) {
 	aggExpressions := []
 
 	for colDef in schemaPerClonotypeNoAggregates {
-		if colDef.column == "clonotypeLabel" {
+		if colDef.column == "clonotypeLabel" || colDef.column == "nLengthTotalAdded" {
 			continue
 		}
 		aggExpressions = append(aggExpressions,
@@ -91,6 +91,14 @@ self.body(func(inputs) {
 
 	aggregatedDf := currentDf.groupBy("clonotypeKey").agg(aggExpressions...)
 
+	// Calculate total added nucleotides: VDJunction + DJJunction for chains with D genes, VJJunction for chains without D genes
+	aggregatedDf = aggregatedDf.withColumns(
+		pt.when(pt.col("nLengthVDJunction").isNotNull().and(pt.col("nLengthVDJunction").neq("no_d_gene"))).
+			then(pt.col("nLengthVDJunction").cast("Int").plus(pt.col("nLengthDJJunction").cast("Int"))).
+			otherwise(pt.col("nLengthVJJunction").cast("Int")).
+			alias("nLengthTotalAdded")
+	)
+
 	aggregatedDf = clonotypeLabel.addClonotypeLabelColumnsPt(aggregatedDf, "clonotypeKey", "clonotypeLabel", pt)
 
 	aggregatedDf.save("output.tsv")

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

@@ -116,7 +116,7 @@ addSpec := func(columns, additionalSpec) {
 // Ordering rules
 //   AA Sequences
 
-calculateExportSpecs := func(presetSpecForBack, blockId) {
+calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
@@ -125,6 +125,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	splitByC := ops.splitByC
 
 	isSingleCell := !is_undefined(cellTags) && len(cellTags) > 0
+	hashCellKey := isSingleCell && len(cellTags) == 1
 
 	assemblingFeatureInfo := assemblingFeatureInfo(assemblingFeature)
 	productiveFeature := assemblingFeatureInfo.productiveFeature
@@ -540,6 +541,52 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		}
 	}
 
+	// Include junction lengths for calculation of total added nucleotides
+	junctionTypes := [ "VJ", "VD", "DJ" ]
+	for junctionType in junctionTypes {
+		feature := junctionType + "Junction"
+		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
+		
+		columnsSpecPerClonotypeNoAggregates += [ {
+			column: "nLength" + feature,
+			id: "n-length-" + text.to_lower(junctionType) + "-junction",
+			naRegex: naRegex,
+			allowNA: true,
+			spec: {
+				name: "pl7.app/vdj/sequenceLength",
+				valueType: "Int",
+				domain: {
+					"pl7.app/vdj/feature": feature,
+					"pl7.app/alphabet": "nucleotide"
+				},
+				annotations: a(orderP, false, {
+					"pl7.app/label": "Length of " + junctionType + " Junction nt"
+				})
+			}
+		} ]
+		exportArgs += [ [ "-nLength", feature ] ]
+		orderP -= 100
+	}
+	
+	// Spec for total added length (calculated by pt in aggregate-by-clonotype-key, no flag)
+	columnsSpecPerClonotypeNoAggregates += [ {
+		column: "nLengthTotalAdded",
+		id: "n-length-total-added",
+		naRegex: "region_not_covered|no_d_gene",
+		allowNA: true,
+		spec: {
+			name: "pl7.app/vdj/sequenceLength",
+			valueType: "Int",
+			domain: {
+				"pl7.app/alphabet": "nucleotide"
+			},
+			annotations: a(orderP, false, {
+				"pl7.app/label": "Total number of added nt"
+			})
+		}
+	} ]
+	orderP -= 100
+
 	// VDJC Hits
 
 	geneHitColumnVariants := [ {
@@ -765,9 +812,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	// Axes
 
-	axesByClonotypeKey := undefined
-	axesByScClonotypeKey := undefined
+	axisByClonotypeKeyGen := undefined
+	axisByScClonotypeKeyGen := undefined
 	cellTagColumns := undefined
+	cellLinkerColumnSettingsGen := undefined
 
 	if !is_undefined(clonotypeKeyColumns) {
 		// checking that corresponding columns exist in export
@@ -785,39 +833,16 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		//   Its absence indicates that merging would be semantically meaningless (e.g., abundance
 		//   measurements specific to each analysis)
 
-		axesByClonotypeKey = [ {
-			column: "clonotypeKey",
-			naRegex: "",
-			spec: {
-				name: "pl7.app/vdj/clonotypeKey",
-				type: "String",
-				domain: {
-					"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture)),
-					"pl7.app/vdj/clonotypingRunId": blockId
-				},
-				annotations: {
-					"pl7.app/label": "Clonotype ID",
-					"pl7.app/table/fontFamily": "monospace",
-					"pl7.app/table/visibility": "default",
-					"pl7.app/table/orderPriority": "110000",
-					"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
-				}
-			}
-		} ]
-
-		if isSingleCell {
-			cellTagColumns = slices.map(cellTags, func(cellTag) {
-				return "tagValue" + cellTag
-			})
-
-			axesByScClonotypeKey = [ {
-				column: "scClonotypeKey",
+		axisByClonotypeKeyGen = func(chain) {
+			return {
+				column: "clonotypeKey",
 				naRegex: "",
 				spec: {
-					name: "pl7.app/vdj/scClonotypeKey",
+					name: "pl7.app/vdj/clonotypeKey",
 					type: "String",
 					domain: {
-						"pl7.app/vdj/scClonotypeKey/structure": string(json.encode(keyStrincture)),
+						"pl7.app/vdj/chain": chain,
+						"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture)),
 						"pl7.app/vdj/clonotypingRunId": blockId
 					},
 					annotations: {
@@ -828,7 +853,69 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
 					}
 				}
-			} ]
+			}
+		}
+
+		if isSingleCell {
+			cellTagColumns = slices.map(cellTags, func(cellTag) {
+				return "tagValue" + cellTag
+			})
+
+			axisByScClonotypeKeyGen = func(receptor) {
+				return {
+					column: "scClonotypeKey",
+					naRegex: "",
+					spec: {
+						name: "pl7.app/vdj/scClonotypeKey",
+						type: "String",
+						domain: {
+							"pl7.app/vdj/receptor": receptor,
+							"pl7.app/vdj/scClonotypeKey/structure": string(json.encode(keyStrincture)),
+							"pl7.app/vdj/clonotypingRunId": blockId
+						},
+						annotations: {
+							"pl7.app/label": "Clonotype ID",
+							"pl7.app/table/fontFamily": "monospace",
+							"pl7.app/table/visibility": "default",
+							"pl7.app/table/orderPriority": "110000",
+							"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
+						}
+					}
+				}
+			}
+
+			cellLinkerColumnSettingsGen = func(receptor) {
+				return {
+					axes: [ {
+						column: "sampleId",
+						spec: sampleIdAxisSpec
+					}, {
+						column: "cellKey",
+						spec: {
+							name: "pl7.app/sc/cellId",
+							type: "String",
+							annotations: a(110000, true, {
+								"pl7.app/label": "Cell ID",
+								"pl7.app/table/fontFamily": "monospace",
+								"pl7.app/parents": string(json.encode([sampleIdAxisSpec.name]))
+							})
+						}
+					}, axisByScClonotypeKeyGen(receptor) ],
+					columns: [ {
+						column: "1",
+						spec: {
+							name: "pl7.app/sc/cellLinker",
+							valueType: "Int",
+							annotations: a(0, undefined, {
+								"pl7.app/label": "Cell Linker",
+								"pl7.app/isLinkerColumn": "true"
+							})
+						}
+					} ],
+					storageFormat: "Binary",
+					partitionKeyLength: 1
+				}
+			}
 
 			//	exportArgs += [ [ "-tags", "Cell" ] ]
 			// 	axesByClonotypeKeyAndCellTag = axesByClonotypeKey + [ {
@@ -851,8 +938,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 		cellTagColumns: cellTagColumns,
 
-		axesByClonotypeKey: axesByClonotypeKey,
-		axesByScClonotypeKey: axesByScClonotypeKey,
+		axisByClonotypeKeyGen: axisByClonotypeKeyGen,
+		axisByScClonotypeKeyGen: axisByScClonotypeKeyGen,
 
 		columnsSpecPerSample: columnsSpecPerSample,
 		columnsSpecPerSampleSc: columnsSpecPerSampleSc,
@@ -870,7 +957,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		mainIsProductiveColumn: mainIsProductiveColumn,
 		mainIsProductiveArgs: mainIsProductiveArgs,
 
-		exportArgs: exportArgs
+		exportArgs: exportArgs,
+
+		hashCellKey: hashCellKey,
+		cellLinkerColumnSettingsGen: cellLinkerColumnSettingsGen
 	}
 }
 

package/src/mixcr-export.tpl.tengo

@@ -1,4 +1,4 @@
-//tengo:hash_override 553D3080-FB87-44BC-BEEB-DB9EB5F773D8
+//tengo:hash_override E5C1AD4C-B44D-4DE1-BBF1-4CB42ED7579A
 
 ll := import("@platforma-sdk/workflow-tengo:ll")
 self := import("@platforma-sdk/workflow-tengo:tpl.light")
@@ -28,6 +28,11 @@ self.body(func(inputs) {
 	clonotypeKeyArgs := params.clonotypeKeyArgs
 
 	cellTagColumns := params.cellTagColumns
+	// if false cell key will not be hashed
+	hashCellKey := params.hashCellKey
+	if !hashCellKey && !is_undefined(cellTagColumns) {
+		ll.assert(len(cellTagColumns) == 1, "cellTagColumns must be a single column when hashCellKey is false")
+	}
 
 	mainAbundanceColumnUnnormalizedArgs := params.mainAbundanceColumnUnnormalizedArgs
 	mainIsProductiveArgs := params.mainIsProductiveArgs
@@ -144,7 +149,7 @@ self.body(func(inputs) {
 
 		dfSingleCell.addColumns(
 			hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey"),
-			hashKeyDerivationExpressionPt(cellTagColumns).alias("cellKey")
+			hashCellKey ? hashKeyDerivationExpressionPt(cellTagColumns).alias("cellKey") : pt.col(cellTagColumns[0]).alias("cellKey")
 		)
 
 		dfSingleCell.save("output.tsv")

package/src/process-single-cell.tpl.tengo

@@ -1,4 +1,4 @@
-//tengo:hash_override 8E4B6062-534D-4322-9CED-EC75E499A10A
+//tengo:hash_override AB9AC8BA-5FFC-40C5-B2F7-AC42181524F5
 
 ll := import("@platforma-sdk/workflow-tengo:ll")
 self := import("@platforma-sdk/workflow-tengo:tpl.light")
@@ -15,7 +15,9 @@ clonotypeLabel := import(":clonotype-label")
 json := import("json")
 math := import("math")
 
-self.defineOutputs("abundanceTsv", "clonotypeTsv", "propertiesAPrimaryTsv", "propertiesASecondaryTsv", "propertiesBPrimaryTsv", "propertiesBSecondaryTsv")
+self.defineOutputs("abundanceTsv", "clonotypeTsv",
+	"propertiesAPrimaryTsv", "propertiesASecondaryTsv", "propertiesBPrimaryTsv", "propertiesBSecondaryTsv",
+	"cellsTsv")
 
 ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptabler:main")
 
@@ -184,6 +186,10 @@ self.body(func(inputs) {
 	)
 	allChainsFilteredDf := allChainsMergedWithScKeyDf.filter(filterCondition)
 
+	allChainsFilteredDf.
+		withColumns(pt.lit(1).alias("1")).
+		save("cells.tsv", {columns: ["sampleId", "cellKey", "scClonotypeKey", "1"]})
+
 	clonotypeTableDf := allChainsFilteredDf.groupBy(
 		"scClonotypeKey", "clonotypeKeyA1", "clonotypeKeyA2", "clonotypeKeyB1", "clonotypeKeyB2"
 	).agg(
@@ -210,6 +216,7 @@ self.body(func(inputs) {
 
 	clonotypeTsv := cellGroupingRunResult.getFile("clonotype.tsv")
 	abundanceTsv := cellGroupingRunResult.getFile("abundance.tsv")
+	cellsTsv := cellGroupingRunResult.getFile("cells.tsv")
 
 	//
 	// Output processing - Reimplemented with PTabler pt API
@@ -303,6 +310,9 @@ self.body(func(inputs) {
 		// used for aggregates (i.e. sampleCount and clonotypeLabel)
 		clonotypeTsv: clonotypeTsv,
 
+		// used to build cell <-> clonotype linker column
+		cellsTsv: cellsTsv,
+
 		// must have scClonotypeKey columns
 		propertiesAPrimaryTsv: outputProcessingRunResult.getFile(chainMappings[0].finalOutFile),
 		propertiesASecondaryTsv: outputProcessingRunResult.getFile(chainMappings[1].finalOutFile),

package/src/process.tpl.tengo

@@ -71,6 +71,7 @@ self.body(func(inputs) {
 	presetCommonName := params.presetCommonName
 	isLibraryFileGzipped := params.isLibraryFileGzipped
 
+	sampleIdAxisSpec := inputSpec.axesSpec[0]
 
 	if is_undefined(presetSpecForBack) {
 		ll.panic("no presetSpecForBack")
@@ -201,7 +202,7 @@ self.body(func(inputs) {
 		}
 	} ]
 
-	exportSpecs := calculateExportSpecs(presetSpecForBack, blockId)
+	exportSpecs := calculateExportSpecs(presetSpecForBack, sampleIdAxisSpec, blockId)
 
 	columnsSpecPerSample := exportSpecs.columnsSpecPerSample
 	columnsSpecPerSampleSc := exportSpecs.columnsSpecPerSampleSc
@@ -214,8 +215,11 @@ self.body(func(inputs) {
 	cellTagColumns := exportSpecs.cellTagColumns
 
 	// axesByClonotypeId := exportSpecs.axesByClonotypeId
-	axesByClonotypeKey := exportSpecs.axesByClonotypeKey
-	axesByScClonotypeKey := exportSpecs.axesByScClonotypeKey
+
+	// function with chain argument
+	axisByClonotypeKeyGen := exportSpecs.axisByClonotypeKeyGen
+	// function with receptor argument
+	axisByScClonotypeKeyGen := exportSpecs.axisByScClonotypeKeyGen
 
 	exportArgs := exportSpecs.exportArgs
 
@@ -227,13 +231,9 @@ self.body(func(inputs) {
 	mainAbundanceColumnNormalizedArgs := exportSpecs.mainAbundanceColumnNormalizedArgs
 	mainAbundanceColumnUnnormalizedArgs := exportSpecs.mainAbundanceColumnUnnormalizedArgs
 
-	if is_undefined(axesByClonotypeKey) {
-		ll.panic("Absent clonotype key not supported")
-	}
-
-	if len(axesByClonotypeKey) != 1 || (!is_undefined(axesByScClonotypeKey) && len(axesByScClonotypeKey) != 1) {
-		ll.panic("Assertion error: expected exactly one clonotype key axis")
-	}
+	hashCellKey := exportSpecs.hashCellKey
+	// function with receptor argument
+	cellLinkerColumnSettingsGen := exportSpecs.cellLinkerColumnSettingsGen
 
 	mixcrResults := pframes.processColumn(
 		{ spec: inputSpec, data: inputs.inputData },
@@ -324,10 +324,6 @@ self.body(func(inputs) {
 		chainInfo := chainInfos[chain]
 		ll.assert(!is_undefined(chainInfo), "chainInfo not found for chain %v", chain)
 
-		axesByClonotypeKeyWithChain := [ maps.deepTransform(axesByClonotypeKey[0], {
-			spec: { domain: { "pl7.app/vdj/chain": chain } }
-		}) ]
-
 		//
 		// Exporting CLNS -> TSV
 		//
@@ -352,7 +348,7 @@ self.body(func(inputs) {
 				type: "Xsv",
 				xsvType: "tsv",
 				settings: {
-					axes: axesByClonotypeKeyWithChain,
+					axes: [ axisByClonotypeKeyGen(chain) ],
 					columns: columnsSpecPerSample,
 					storageFormat: "Binary",
 					partitionKeyLength: 0
@@ -407,6 +403,8 @@ self.body(func(inputs) {
 						mainAbundanceColumnUnnormalizedArgs: mainAbundanceColumnUnnormalizedArgs,
 
 						cellTagColumns: cellTagColumns,
+						hashCellKey: hashCellKey,
+
 						exportArgs: exportArgs,
 						isLibraryFileGzipped: isLibraryFileGzipped
 					},
@@ -441,7 +439,7 @@ self.body(func(inputs) {
 				type: "Xsv",
 				xsvType: "tsv",
 				settings: {
-					axes: axesByClonotypeKeyWithChain,
+					axes: [ axisByClonotypeKeyGen(chain) ],
 					columns: columnsSpecPerClonotypeNoAggregates + columnsSpecPerClonotypeAggregates,
 					storageFormat: "Binary",
 					partitionKeyLength: 0
@@ -502,10 +500,6 @@ self.body(func(inputs) {
 		for receptor in receptors {
 			receptorInfo := receptorInfos[receptor]
 
-			axesByScClonotypeKeyWithReceptor := [ maps.deepTransform(axesByScClonotypeKey[0], {
-				spec: { domain: { "pl7.app/vdj/receptor": receptor } }
-			}) ]
-
 			singleCellOutputs := [ {
 				type: "Resource",
 				spec: {
@@ -524,8 +518,8 @@ self.body(func(inputs) {
 				settings: {
 					axes: [ {
 						column: "sampleId",
-						spec: inputSpec.axesSpec[0]
-					} ] + axesByScClonotypeKeyWithReceptor,
+						spec: sampleIdAxisSpec
+					}, axisByScClonotypeKeyGen(receptor) ],
 					columns: columnsSpecPerSampleSc,
 					storageFormat: "Binary",
 					partitionKeyLength: 1
@@ -538,7 +532,7 @@ self.body(func(inputs) {
 				type: "Xsv",
 				xsvType: "tsv",
 				settings: {
-					axes: axesByScClonotypeKeyWithReceptor,
+					axes: [ axisByScClonotypeKeyGen(receptor) ],
 					columns: columnsSpecPerClonotypeSc,
 					storageFormat: "Binary"
 				},
@@ -599,7 +593,7 @@ self.body(func(inputs) {
 						type: "Xsv",
 						xsvType: "tsv",
 						settings: {
-							axes: axesByScClonotypeKeyWithReceptor,
+							axes: [ axisByScClonotypeKeyGen(receptor) ],
 							columns: transformSpecs(isPrimary ? columnsSpecPerClonotypeNoAggregates : columnsSpecPerClonotypeSecondary, {
 								spec: {
 									domain: {
@@ -620,6 +614,16 @@ self.body(func(inputs) {
 				}
 			}
 
+			singleCellOutputs += [ {
+				type: "Xsv",
+				xsvType: "tsv",
+				settings: cellLinkerColumnSettingsGen(receptor),
+				mem: "16GiB",
+				cpu: 2,
+				name: "cellsLinkerTable",
+				path: ["cellsTsv"]
+			} ]
+
 			chainA := receptorInfo.chains[0]
 			chainB := receptorInfo.chains[1]
 
@@ -669,6 +673,8 @@ self.body(func(inputs) {
 			singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesASecondary", "clonotypeProperties/" + receptor + "/aSecondary/")
 			singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBPrimary", "clonotypeProperties/" + receptor + "/bPrimary/")
 			singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBSecondary", "clonotypeProperties/" + receptor + "/bSecondary/")
+
+			singleCellResult.addXsvOutputToBuilder(clonotypes, "cellsLinkerTable", "clonotypeProperties/" + receptor + "/cellsLinkerTable/")
 		}
 	}
 

package/src/test/columns-calculate.tpl.tengo

@@ -1,5 +1,6 @@
 self := import("@platforma-sdk/workflow-tengo:tpl.light")
 ll := import("@platforma-sdk/workflow-tengo:ll")
+maps := import("@platforma-sdk/workflow-tengo:maps")
 
 calculateExportSpecs := import(":calculate-export-specs")
 
@@ -8,7 +9,12 @@ self.defineOutputs("exportSpecs")
 self.body(func(inputs) {
 	presetSpecForBack := inputs.presetSpecForBack.getDataAsJson()
 
-	exportSpecs := calculateExportSpecs(presetSpecForBack, "test")
+	exportSpecs := calculateExportSpecs(presetSpecForBack, {}, "test")
+	exportSpecs = maps.deepMerge(exportSpecs, {
+    	axisByClonotypeKeyGen: undefined,
+		axisByScClonotypeKeyGen: undefined,
+		cellLinkerColumnSettingsGen: undefined
+	})
 
 	return {
 		exportSpecs: exportSpecs