@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.0.1 → 2.1.1

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.1 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@2.0.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.1 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) 47946ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11920ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 7407ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7323ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7314ms
-   ✓ checking preset for 'rna-seq' 6897ms
-   ✓ checking preset for 'generic-single-cell-gex' 7083ms
+ ✓ src/test/columns.test.ts (6 tests) 49169ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13728ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 7394ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7337ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7115ms
+   ✓ checking preset for 'rna-seq' 6700ms
+   ✓ checking preset for 'generic-single-cell-gex' 6894ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  11:38:19
-   Duration  48.72s (transform 43ms, setup 0ms, collect 544ms, tests 47.95s, environment 0ms, prepare 72ms)
+   Start at  18:50:45
+   Duration  49.93s (transform 43ms, setup 0ms, collect 537ms, tests 49.17s, environment 0ms, prepare 56ms)
 

package/CHANGELOG.md

@@ -1,5 +1,20 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 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
+
+- a168fe3: pl7.app/abundance/isPrimary and pl7.app/isAnchor annotations added to the output columns
+
 ## 2.0.1
 
 ### Patch 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")
@@ -118,6 +119,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
+				"pl7.app/isAnchor": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -134,6 +137,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -157,7 +161,9 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
-						"pl7.app/label": "Number of UMI"
+						"pl7.app/abundance/isPrimary": "true",
+						"pl7.app/isAnchor": "true",
+						"pl7.app/label": "Number of UMIs"
 					})
 				}
 			}, {
@@ -173,7 +179,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
-						"pl7.app/label": "Fraction of UMI"
+						"pl7.app/abundance/isPrimary": "true",
+						"pl7.app/label": "Fraction of UMIs"
 					})
 				}
 			} ]
@@ -229,13 +236,19 @@ 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] ) {
@@ -450,6 +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/blockId": blockId
+	} } })
+
+
+
+
+
+
+	columnsSpecPerClonotype = addSpec(columnsSpecPerClonotype, { spec: {
+		domain: {
+			"pl7.app/blockId": blockId
+		},
+		annotations: {
+			"pl7.app/segmentedBy": string(json.encode(["pl7.app/blockId"]))
+		}
+	} })
+
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype
 
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.0.1",
+  "version": "2.1.1",
   "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")
@@ -118,6 +119,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
+				"pl7.app/isAnchor": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -134,6 +137,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": !hasUmi ? "true" : undefined,
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -157,7 +161,9 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
-						"pl7.app/label": "Number of UMI"
+						"pl7.app/abundance/isPrimary": "true",
+						"pl7.app/isAnchor": "true",
+						"pl7.app/label": "Number of UMIs"
 					})
 				}
 			}, {
@@ -173,7 +179,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
-						"pl7.app/label": "Fraction of UMI"
+						"pl7.app/abundance/isPrimary": "true",
+						"pl7.app/label": "Fraction of UMIs"
 					})
 				}
 			} ]
@@ -229,13 +236,19 @@ 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] ) {
@@ -450,6 +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/blockId": 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/blockId": blockId
+		},
+		annotations: {
+			"pl7.app/segmentedBy": string(json.encode(["pl7.app/blockId"]))
+		}
+	} })
+
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype
 
 	// Creating a column map for fast search

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 })
 	}
 })
@@ -93,7 +93,10 @@ 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
+	}
 
 	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

@@ -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) {
@@ -214,6 +215,7 @@ 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,
@@ -242,6 +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: {