@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.0.0 → 2.1.0

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 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@2.0.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 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) 48242ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11740ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 7636ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7348ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7318ms
-   ✓ checking preset for 'rna-seq' 7099ms
-   ✓ checking preset for 'generic-single-cell-gex' 7100ms
+ ✓ 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
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  16:45:52
-   Duration  48.98s (transform 48ms, setup 0ms, collect 509ms, tests 48.24s, environment 0ms, prepare 63ms)
+   Start at  20:11:15
+   Duration  48.92s (transform 45ms, setup 0ms, collect 537ms, tests 48.16s, environment 0ms, prepare 61ms)
 

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.1.0
+
+### Minor Changes
+
+- a168fe3: pl7.app/abundance/isPrimary and pl7.app/isAnchor annotations added to the output columns
+
+## 2.0.1
+
+### Patch Changes
+
+- 6c45177: Chain is added to output columns domain
+- Updated dependencies [6c45177]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder@1.0.1
+
 ## 2.0.0
 
 ### Major Changes

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

@@ -107,37 +107,39 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 	columnsSpecPerSample += [ {
-			column: "readCount",
-			id: "read-count",
-			allowNA: false,
-			spec: {
-				name: "pl7.app/vdj/readCount",
-				valueType: "Long",
-				annotations: a(90000, !hasUmi, {
-					"pl7.app/min": "1",
-					"pl7.app/isAbundance": "true",
-					"pl7.app/abundance/unit": "reads",
-					"pl7.app/abundance/normalized": "false",
-					"pl7.app/label": "Number Of Reads"
-				})
-			}
-		}, {
-			column: "readFraction",
-			id: "read-fraction",
-			allowNA: false,
-			spec: {
-				name: "pl7.app/vdj/readFraction",
-				valueType: "Double",
-				annotations: a(89000, !hasUmi, {
-					"pl7.app/min": "0",
-					"pl7.app/max": "1",
-					"pl7.app/isAbundance": "true",
-					"pl7.app/abundance/unit": "reads",
-					"pl7.app/abundance/normalized": "true",
-					"pl7.app/label": "Fraction of reads"
-				})
-			}
-		} ]
+		column: "readCount",
+		id: "read-count",
+		allowNA: false,
+		spec: {
+			name: "pl7.app/vdj/readCount",
+			valueType: "Long",
+			annotations: a(90000, !hasUmi, {
+				"pl7.app/min": "1",
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/unit": "reads",
+				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/label": "Number Of Reads"
+			})
+		}
+	}, {
+		column: "readFraction",
+		id: "read-fraction",
+		allowNA: false,
+		spec: {
+			name: "pl7.app/vdj/readFraction",
+			valueType: "Double",
+			annotations: a(89000, !hasUmi, {
+				"pl7.app/min": "0",
+				"pl7.app/max": "1",
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/unit": "reads",
+				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/label": "Fraction of reads"
+			})
+		}
+	} ]
 	exportArgs += [
 		[ "-readCount" ],
 		[ "-readFraction" ]
@@ -157,6 +159,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Number of UMI"
 					})
 				}
@@ -173,6 +176,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Fraction of UMI"
 					})
 				}
@@ -229,13 +233,19 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
+
+	anchorFeature := undefined;
+
 	features := undefined
 	if is_undefined(assemblingFeature) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
 		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
+		anchorFeature = "CDR3"
 	}
 
 	for isImputed in ( is_undefined(assemblingFeature) ? [false, true] : [false] ) {
@@ -248,6 +258,13 @@ 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" : ""),
@@ -259,10 +276,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, {
-								"pl7.app/vdj/imputed": string(isImputed),
-								"pl7.app/label": featureU + " " + alphabetShort
-							})
+							annotations: a(orderP, visibility, annotations)
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]

package/package.json

@@ -1,15 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "description": "Tengo-based template",
+  "dependencies": {
+    "@platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder": "1.0.1"
+  },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^1.19.2",
-    "@platforma-sdk/workflow-tengo": "^2.15.4",
+    "@platforma-sdk/workflow-tengo": "^2.15.6",
     "@milaboratories/software-pframes-conv": "2.1.16",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.15.11",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.15.15",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-147-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.22.84",
+    "@platforma-sdk/test": "^1.22.87",
     "vitest": "^2.1.8",
     "typescript": "~5.5.4"
   },

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

@@ -107,37 +107,39 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	// Abundance
 
 	columnsSpecPerSample += [ {
-			column: "readCount",
-			id: "read-count",
-			allowNA: false,
-			spec: {
-				name: "pl7.app/vdj/readCount",
-				valueType: "Long",
-				annotations: a(90000, !hasUmi, {
-					"pl7.app/min": "1",
-					"pl7.app/isAbundance": "true",
-					"pl7.app/abundance/unit": "reads",
-					"pl7.app/abundance/normalized": "false",
-					"pl7.app/label": "Number Of Reads"
-				})
-			}
-		}, {
-			column: "readFraction",
-			id: "read-fraction",
-			allowNA: false,
-			spec: {
-				name: "pl7.app/vdj/readFraction",
-				valueType: "Double",
-				annotations: a(89000, !hasUmi, {
-					"pl7.app/min": "0",
-					"pl7.app/max": "1",
-					"pl7.app/isAbundance": "true",
-					"pl7.app/abundance/unit": "reads",
-					"pl7.app/abundance/normalized": "true",
-					"pl7.app/label": "Fraction of reads"
-				})
-			}
-		} ]
+		column: "readCount",
+		id: "read-count",
+		allowNA: false,
+		spec: {
+			name: "pl7.app/vdj/readCount",
+			valueType: "Long",
+			annotations: a(90000, !hasUmi, {
+				"pl7.app/min": "1",
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/unit": "reads",
+				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/label": "Number Of Reads"
+			})
+		}
+	}, {
+		column: "readFraction",
+		id: "read-fraction",
+		allowNA: false,
+		spec: {
+			name: "pl7.app/vdj/readFraction",
+			valueType: "Double",
+			annotations: a(89000, !hasUmi, {
+				"pl7.app/min": "0",
+				"pl7.app/max": "1",
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/unit": "reads",
+				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
+				"pl7.app/label": "Fraction of reads"
+			})
+		}
+	} ]
 	exportArgs += [
 		[ "-readCount" ],
 		[ "-readFraction" ]
@@ -157,6 +159,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Number of UMI"
 					})
 				}
@@ -173,6 +176,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Fraction of UMI"
 					})
 				}
@@ -229,13 +233,19 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	// Sequences
 
+	// column with nucleotide sequence of this feature will be marked as anchor
+	anchorFeature := undefined;
+
 	features := undefined
 	if is_undefined(assemblingFeature) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
 		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
+		anchorFeature = "CDR3"
 	}
 
 	for isImputed in ( is_undefined(assemblingFeature) ? [false, true] : [false] ) {
@@ -248,6 +258,13 @@ 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" : ""),
@@ -259,10 +276,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, {
-								"pl7.app/vdj/imputed": string(isImputed),
-								"pl7.app/label": featureU + " " + alphabetShort
-							})
+							annotations: a(orderP, visibility, annotations)
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]

package/src/main.tpl.tengo

@@ -20,7 +20,7 @@ processTpl := assets.importTemplate(":process")
 wf.setPreRun(assets.importTemplate(":prerun"))
 
 wf.prepare(func(args){
-	return{
+	return {
 		resolvedLibraryInput: wf.resolve(args.inputLibrary, { errIfMissing: false })
 	}
 })
@@ -93,13 +93,10 @@ wf.body(func(args) {
 	presetSpecForBack := presetInfoResult.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 
 	// calculating chains
-	chains := [
-		{ name: "IGH", mixcrChain: "IGH" },
-		{ name: "IGKL", mixcrChain: "IGK,IGL" },
-		{ name: "TRA", mixcrChain: "TRA" },
-		{ name: "TRB", mixcrChain: "TRB" },
-		{ name: "TRD", mixcrChain: "TRD" },
-		{ name: "TRG", mixcrChain: "TRG" } ]
+	chains := ["IGHeavy", "IGLight", "TRA", "TRB", "TRD", "TRG"]
+	if !is_undefined(args.chains) {
+		chains = args.chains
+	}
 
 	runMixcr := render.createEphemeral(processTpl, {
 		inputSpec: input.getFutureInputField("spec"),

package/src/mixcr-export.tpl.tengo

@@ -23,6 +23,7 @@ self.body(func(inputs) {
 	// Exporting clones from clns file
 
 	mixcrCmdBuilder := exec.builder().
+		inMediumQueue().
 		printErrStreamToStdout().
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").

package/src/process.tpl.tengo

@@ -7,6 +7,7 @@ assets := import("@platforma-sdk/workflow-tengo:assets")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
 smart := import("@platforma-sdk/workflow-tengo:smart")
 slices := import("@platforma-sdk/workflow-tengo:slices")
+maps := import("@platforma-sdk/workflow-tengo:maps")
 file := import("@platforma-sdk/workflow-tengo:file")
 llPFrames := import("@platforma-sdk/workflow-tengo:pframes.ll")
 pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
@@ -28,6 +29,21 @@ self.awaitState("inputSpec", "ResourceReady")
 self.awaitState("presetSpecForBack", "ResourceReady")
 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" }
+}
+
+receptorInfo := {
+	"IG": { chains: ["IGHeavy", "IGLight"], name: "IG" },
+	"TRAB": { chains: ["TRB", "TRA"], name: "TRAB" },
+	"TRGD": { chains: ["TRD", "TRG"], name: "TRGD" }
+}
+
 self.body(func(inputs) {
 
 	inputSpec := inputs.inputSpec
@@ -198,6 +214,7 @@ self.body(func(inputs) {
 				name: "pl7.app/sequencing/readIndex",
 				optional: true
 			}],
+
 			// resulting aggregation axes names will be checked against supported combinations
 			// in the body template
 			passAggregationAxesNames: true,
@@ -225,6 +242,22 @@ self.body(func(inputs) {
 	clonotypes := pframes.pFrameBuilder()
 
 	for chain in chains {
+		chainInfo := chainInfos[chain]
+		additionalSpec := {
+			spec: {
+				domain: {
+					"pl7.app/chain": chain
+				}
+			}
+		}
+		columnSpecsTransform := func(specs) {
+			return slices.map(specs, func(spec) {
+				return maps.deepMerge(spec, additionalSpec)
+			})
+		}
+
+		traceSteps := [{type: "milaboratories.mixcr-clonotyping.export", id: blockId + "." + chain, importance: 80, label: chainInfo.name}]
+
 		exportOutputs := [ {
 			type: "Resource",
 			spec: {
@@ -237,17 +270,6 @@ self.body(func(inputs) {
 			},
 			name: "clonotypeTable",
 			path: ["tsv"]
-		// }, {
-		// 	type: "Xsv",
-		// 	xsvType: "tsv",
-		// 	settings: {
-		// 		axes: axesByClonotypeId,
-		// 		columns: columnsSpec,
-		// 		storageFormat: "Binary",
-		// 		partitionKeyLength: 0
-		// 	},
-		// 	name: "byCloneId",
-		// 	path: ["tsv"]
 		} ]
 
 		if !is_undefined(axesByClonotypeKey) {
@@ -256,7 +278,7 @@ self.body(func(inputs) {
 				xsvType: "tsv",
 				settings: {
 					axes: axesByClonotypeKey,
-					columns: columnsSpecPerSample,
+					columns: columnSpecsTransform(columnsSpecPerSample),
 					storageFormat: "Binary",
 					partitionKeyLength: 0
 				},
@@ -271,11 +293,11 @@ self.body(func(inputs) {
 			exportOutputs,
 			{
 				// will be automatically propagated to all output specs
-				traceSteps: [{type: "milaboratories.mixcr-clonotyping.export", id: blockId + "." + chain.name, importance: 80, label: chain.name}],
+				traceSteps: traceSteps,
 
 				extra: {
 					params: {
-						chains: chain.mixcrChain,
+						chains: chainInfo.mixcrFilter,
 						clonotypeKeyColumns: clonotypeKeyColumns,
 						exportArgs: exportArgs
 					}
@@ -283,15 +305,14 @@ self.body(func(inputs) {
 			}
 		)
 
-		// exportResults.addXsvOutputToBuilder(clonotypes, "byCloneId", "byCloneId/" + chain.name + "/")
-		exportResults.addXsvOutputToBuilder(clonotypes, "byCloneKeyBySample", "byCloneKeyBySample/" + chain.name + "/")
+		exportResults.addXsvOutputToBuilder(clonotypes, "byCloneKeyBySample", "byCloneKeyBySample/" + chain + "/")
 
 		aggregationOutputs := [ {
 			type: "Xsv",
 			xsvType: "tsv",
 			settings: {
 				axes: axesByClonotypeKey,
-				columns: columnsSpecPerClonotype,
+				columns: columnSpecsTransform(columnsSpecPerClonotype),
 				storageFormat: "Binary",
 				partitionKeyLength: 0
 			},
@@ -316,7 +337,7 @@ self.body(func(inputs) {
 			}
 		)
 
-		aggregateByCloneKey.addXsvOutputToBuilder(clonotypes, "byCloneKey", "byCloneKey/" + chain.name + "/")
+		aggregateByCloneKey.addXsvOutputToBuilder(clonotypes, "byCloneKey", "byCloneKey/" + chain + "/")
 	}
 
 	return {