@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.1.0 → 2.2.0

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...

package/.turbo/turbo-test.log

@@ -1,20 +1,20 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > vitest
 
 
  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 48155ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11939ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 7604ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7330ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7316ms
-   ✓ checking preset for 'rna-seq' 6894ms
-   ✓ checking preset for 'generic-single-cell-gex' 7071ms
+ ✓ src/test/columns.test.ts (6 tests) 49261ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12586ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 7814ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7347ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7319ms
+   ✓ checking preset for 'rna-seq' 6912ms
+   ✓ checking preset for 'generic-single-cell-gex' 7281ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  20:11:15
-   Duration  48.92s (transform 45ms, setup 0ms, collect 537ms, tests 48.16s, environment 0ms, prepare 61ms)
+   Start at  08:44:46
+   Duration  50.16s (transform 54ms, setup 0ms, collect 636ms, tests 49.26s, environment 0ms, prepare 69ms)
 

package/CHANGELOG.md

@@ -1,5 +1,20 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.2.0
+
+### Minor Changes
+
+- 4b82d2d: Source domain for output columns changed from pl7.app/blockId to pl7.app/vdj/clonotypingRunId
+
+## 2.1.1
+
+### Patch Changes
+
+- aed9be8: Fixes trace information propagation
+  Enhances export specifications by adding block and segment annotations
+  Updates abundance labels
+  Refines chain names in the model
+
 ## 2.1.0
 
 ### Minor Changes

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

@@ -1,4 +1,5 @@
 maps := import("@platforma-sdk/workflow-tengo:maps")
+slices := import("@platforma-sdk/workflow-tengo:slices")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 text := import("text")
 json := import("json")
@@ -118,7 +119,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
-				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
+				"pl7.app/isAnchor": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -135,7 +137,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
-				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -160,7 +162,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
 						"pl7.app/abundance/isPrimary": "true",
-						"pl7.app/label": "Number of UMI"
+						"pl7.app/isAnchor": "true",
+						"pl7.app/label": "Number of UMIs"
 					})
 				}
 			}, {
@@ -177,7 +180,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
 						"pl7.app/abundance/isPrimary": "true",
-						"pl7.app/label": "Fraction of UMI"
+						"pl7.app/label": "Fraction of UMIs"
 					})
 				}
 			} ]
@@ -258,13 +261,6 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
-				annotations :=  {
-					"pl7.app/vdj/imputed": string(isImputed),
-					"pl7.app/label": featureU + " " + alphabetShort
-				}
-				if featureU == anchorFeature && !isImputed && !isAminoAcid {
-					annotations["pl7.app/isAnchor"] = "true"
-				}
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -276,7 +272,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, annotations)
+							annotations: a(orderP, visibility, {
+								"pl7.app/vdj/imputed": string(isImputed),
+								"pl7.app/label": featureU + " " + alphabetShort
+							})
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
@@ -464,6 +463,32 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
+
+
+	addSpec := func(columns, additionalSpec) {
+		return slices.map(columns, func(columnSpec) {
+			return maps.deepMerge(columnSpec, additionalSpec)
+		})
+	}
+
+	columnsSpecPerSample = addSpec(columnsSpecPerSample, { spec: { domain: {
+		"pl7.app/vdj/clonotypingRunId": blockId
+	} } })
+
+
+
+
+
+
+	columnsSpecPerClonotype = addSpec(columnsSpecPerClonotype, { spec: {
+		domain: {
+			"pl7.app/vdj/clonotypingRunId": blockId
+		},
+		annotations: {
+			"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
+		}
+	} })
+
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype
 
 
@@ -542,7 +567,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						type: "String",
 						domain: {
 							"pl7.app/vdj/cellTagId": tag,
-							"pl7.app/blockId": blockId
+							"pl7.app/vdj/clonotypingRunId": blockId
 						},
 						annotations: a(orderP, true, {
 							"pl7.app/label": label

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder": "1.0.1"
@@ -9,16 +9,17 @@
     "@platforma-sdk/tengo-builder": "^1.19.2",
     "@platforma-sdk/workflow-tengo": "^2.15.6",
     "@milaboratories/software-pframes-conv": "2.1.16",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.15.15",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.15.16",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-147-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.22.87",
+    "@platforma-sdk/test": "^1.22.100",
     "vitest": "^2.1.8",
     "typescript": "~5.5.4"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",
     "format": "/usr/bin/env emacs --script ./format.el",
-    "test": "vitest"
+    "test": "vitest",
+    "do-pack": "rm -f *.tgz && pnpm pack && mv *.tgz package.tgz"
   }
 }

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

@@ -1,4 +1,5 @@
 maps := import("@platforma-sdk/workflow-tengo:maps")
+slices := import("@platforma-sdk/workflow-tengo:slices")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 text := import("text")
 json := import("json")
@@ -118,7 +119,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
-				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
+				"pl7.app/isAnchor": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -135,7 +137,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
-				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -160,7 +162,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
 						"pl7.app/abundance/isPrimary": "true",
-						"pl7.app/label": "Number of UMI"
+						"pl7.app/isAnchor": "true",
+						"pl7.app/label": "Number of UMIs"
 					})
 				}
 			}, {
@@ -177,7 +180,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
 						"pl7.app/abundance/isPrimary": "true",
-						"pl7.app/label": "Fraction of UMI"
+						"pl7.app/label": "Fraction of UMIs"
 					})
 				}
 			} ]
@@ -258,13 +261,6 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
-				annotations :=  {
-					"pl7.app/vdj/imputed": string(isImputed),
-					"pl7.app/label": featureU + " " + alphabetShort
-				}
-				if featureU == anchorFeature && !isImputed && !isAminoAcid {
-					annotations["pl7.app/isAnchor"] = "true"
-				}
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -276,7 +272,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, annotations)
+							annotations: a(orderP, visibility, {
+								"pl7.app/vdj/imputed": string(isImputed),
+								"pl7.app/label": featureU + " " + alphabetShort
+							})
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
@@ -464,6 +463,32 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	// All columns are added
 
+	// Adding block and segment annotations
+
+	addSpec := func(columns, additionalSpec) {
+		return slices.map(columns, func(columnSpec) {
+			return maps.deepMerge(columnSpec, additionalSpec)
+		})
+	}
+
+	columnsSpecPerSample = addSpec(columnsSpecPerSample, { spec: { domain: {
+		"pl7.app/vdj/clonotypingRunId": blockId
+	} } })
+
+	//   "pl7.app/segmentedBy" annotation indicates columns that can be meaningfully merged across
+	//   different runs (given they have the same name and axes signature).
+	//   Its absence indicates that merging would be semantically meaningless (e.g., abundance
+	//   measurements specific to each analysis)
+
+	columnsSpecPerClonotype = addSpec(columnsSpecPerClonotype, { spec: {
+		domain: {
+			"pl7.app/vdj/clonotypingRunId": blockId
+		},
+		annotations: {
+			"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
+		}
+	} })
+
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype
 
 	// Creating a column map for fast search
@@ -542,7 +567,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						type: "String",
 						domain: {
 							"pl7.app/vdj/cellTagId": tag,
-							"pl7.app/blockId": blockId
+							"pl7.app/vdj/clonotypingRunId": blockId
 						},
 						annotations: a(orderP, true, {
 							"pl7.app/label": label

package/src/main.tpl.tengo

@@ -93,7 +93,7 @@ wf.body(func(args) {
 	presetSpecForBack := presetInfoResult.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 
 	// calculating chains
-	chains := ["IGHeavy", "IGLight", "TRA", "TRB", "TRD", "TRG"]
+	chains := ["IGHeavy", "IGLight", "TRAlpha", "TRBeta", "TRGamma", "TRDelta"]
 	if !is_undefined(args.chains) {
 		chains = args.chains
 	}

package/src/process.tpl.tengo

@@ -32,16 +32,17 @@ self.awaitState("presetContent", "ResourceReady")
 chainInfos := {
 	"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy" },
 	"IGLight": { mixcrFilter: "IGK,IGL", name: "IG Light" },
-	"TRA": { mixcrFilter: "TRA", name: "TRA" },
-	"TRB": { mixcrFilter: "TRB", name: "TRB" },
-	"TRD": { mixcrFilter: "TRD", name: "TRD" },
-	"TRG": { mixcrFilter: "TRG", name: "TRG" }
+	"TRAlpha": { mixcrFilter: "TRA", name: "TR Alpha" },
+	"TRBeta": { mixcrFilter: "TRB", name: "TR Beta" },
+	"TRGamma": { mixcrFilter: "TRD", name: "TR Gamma" },
+	"TRDelta": { mixcrFilter: "TRG", name: "TR Delta" }
 }
 
+// TODO better naming
 receptorInfo := {
 	"IG": { chains: ["IGHeavy", "IGLight"], name: "IG" },
-	"TRAB": { chains: ["TRB", "TRA"], name: "TRAB" },
-	"TRGD": { chains: ["TRD", "TRG"], name: "TRGD" }
+	"TRAB": { chains: ["TRAlpha", "TRBeta"], name: "TRAB" },
+	"TRGD": { chains: ["TRGamma", "TRDelta"], name: "TRGD" }
 }
 
 self.body(func(inputs) {
@@ -131,7 +132,7 @@ self.body(func(inputs) {
 			valueType: "File",
 			name: "mixcr.com/qc",
 			domain: {
-				"pl7.app/blockId": blockId
+				"pl7.app/vdj/clonotypingRunId": blockId
 			}
 		},
 		name: "qc"
@@ -141,7 +142,7 @@ self.body(func(inputs) {
 			kind: "PColumn",
 			name: "pl7.app/log",
 			domain: {
-				"pl7.app/blockId": blockId
+				"pl7.app/vdj/clonotypingRunId": blockId
 			},
 			valueType: "Log"
 		},
@@ -152,7 +153,7 @@ self.body(func(inputs) {
 			kind: "PColumn",
 			name: "mixcr.com/clns",
 			domain: {
-				"pl7.app/blockId": blockId
+				"pl7.app/vdj/clonotypingRunId": blockId
 			},
 			annotations: clnsAnnotations,
 			valueType: "File"
@@ -165,7 +166,7 @@ self.body(func(inputs) {
 			kind: "PColumn",
 			name: "mixcr.com/report",
 			domain: {
-				"pl7.app/blockId": blockId
+				"pl7.app/vdj/clonotypingRunId": blockId
 			},
 			valueType: "File",
 			axesSpec: [ {
@@ -243,6 +244,7 @@ self.body(func(inputs) {
 
 	for chain in chains {
 		chainInfo := chainInfos[chain]
+		ll.assert(!is_undefined(chainInfo), "chainInfo not found for chain %v", chain)
 		additionalSpec := {
 			spec: {
 				domain: {
@@ -264,7 +266,7 @@ self.body(func(inputs) {
 				kind: "PColumn",
 				name: "mixcr.com/clonotypeTable",
 				domain: {
-					"pl7.app/blockId": blockId
+					"pl7.app/vdj/clonotypingRunId": blockId
 				},
 				valueType: "File"
 			},