@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.19.1 → 2.19.3

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@2.19.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.19.3 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
 
+## 2.19.3
+
+### Patch Changes
+
+- 865b5f5: Added cpu and ram requirements
+
+## 2.19.2
+
+### Patch Changes
+
+- fc18b70: SDK Upgrade: fixes await logic and prevents unexpected freezes
+
 ## 2.19.1
 
 ### Patch Changes

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.19.1",
+  "version": "2.19.3",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.6.3",
+    "@platforma-sdk/workflow-tengo": "^4.7.4",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-169-develop"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.1.6",
-    "@platforma-sdk/test": "^1.32.4",
+    "@platforma-sdk/tengo-builder": "^2.1.10",
+    "@platforma-sdk/test": "^1.34.3",
     "vitest": "~2.1.9",
     "typescript": "~5.5.4"
   },

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

@@ -3,8 +3,10 @@ self := import("@platforma-sdk/workflow-tengo:tpl")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
 slices := import("@platforma-sdk/workflow-tengo:slices")
 maps := import("@platforma-sdk/workflow-tengo:maps")
+units := import("@platforma-sdk/workflow-tengo:units")
 clonotypeLabel := import(":clonotype-label")
 pt := import("@platforma-sdk/workflow-tengo:pt")
+math := import("math")
 
 json := import("json")
 
@@ -24,10 +26,15 @@ self.body(func(inputs) {
 	schemaPerClonotypeNoAggregates := params.schemaPerClonotypeNoAggregates
 	schemaPerSample := params.schemaPerSample
 
-	wf := pt.workflow()
-	dataFrames := []
-
 	inputMap := inputData.inputs()
+	numberOfSamples := len(inputMap)
+
+	wf := pt.workflow().
+		inMediumQueue().
+		mem(int(math.max(numberOfSamples, 64)) * units.GiB).
+		cpu(int(math.max(numberOfSamples, 32)))
+
+	dataFrames := []
 
 	baseSchemaForRead := schemaPerSample + [ { column: "clonotypeKey", type: "String" } ]
 

package/src/mixcr-analyze.tpl.tengo

@@ -64,6 +64,8 @@ self.body(func(inputs) {
 		printErrStreamToStdout().
 		env("MI_PROGRESS_PREFIX", progressPrefix).
 		software(mixcrSw).
+		mem("64GiB").
+		cpu(32).
 		secret("MI_LICENSE", "MI_LICENSE").
 		arg("analyze")
 

package/src/mixcr-export.tpl.tengo

@@ -43,6 +43,8 @@ self.body(func(inputs) {
 	createExport := func(additionalAction) {
 		mixcrCmdBuilder := exec.builder().
 			inMediumQueue().
+			ram("6GiB").
+		    cpu(2).
 			printErrStreamToStdout().
 			dontSaveStdoutOrStderr().
 			software(mixcrSw).
@@ -92,7 +94,11 @@ self.body(func(inputs) {
 	}
 
 	// PTabler processing for main TSV output
-	wfMain := pt.workflow()
+	wfMain := pt.workflow().
+		inMediumQueue().
+		mem("4GiB").
+		cpu(2)
+
 	frameInputMap := {
 		file: unprocessedTsv,
 		xsvType: "tsv",
@@ -128,7 +134,11 @@ self.body(func(inputs) {
 		unprocessedTsvForSingleCell := mixcrForSingleCell.getFile("clones.tsv")
 
 		// PTabler processing for single-cell TSV output
-		wfSingleCell := pt.workflow()
+		wfSingleCell := pt.workflow().
+			inMediumQueue().
+			mem("2GiB").
+			cpu(2)
+
 		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, { xsvType: "tsv", inferSchema: false })
 
 		dfSingleCell.addColumns(

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

@@ -6,7 +6,9 @@ exec := import("@platforma-sdk/workflow-tengo:exec")
 maps := import("@platforma-sdk/workflow-tengo:maps")
 slices := import("@platforma-sdk/workflow-tengo:slices")
 clonotypeLabel := import(":clonotype-label")
+units := import("@platforma-sdk/workflow-tengo:units")
 json := import("json")
+math := import("math")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 
 self.defineOutputs("abundanceTsv", "clonotypeTsv", "propertiesAPrimaryTsv", "propertiesASecondaryTsv", "propertiesBPrimaryTsv", "propertiesBSecondaryTsv")
@@ -37,10 +39,16 @@ self.body(func(inputs) {
 	 * @return the output file
 	 */
 	preprocessByCell := func(byCellTag) {
-		wf := pt.workflow()
+		inputMap := byCellTag.inputs()
+		numberOfSamples := len(inputMap)
+
+		wf := pt.workflow().
+			inMediumQueue().
+			mem(int(math.max(numberOfSamples, 32)) * units.GiB).
+			cpu(int(math.max(numberOfSamples, 16)))
+
 		sampleDataFrames := []
 
-		inputMap := byCellTag.inputs()
 		maps.forEach(inputMap, func(sKey, inputFile) {
 			key := json.decode(sKey)
 			ll.assert(len(key) == 1, "preprocessByCell: byCellTag key should have one element, got %v", key)

package/src/process.tpl.tengo

@@ -340,6 +340,8 @@ self.body(func(inputs) {
 					storageFormat: "Binary",
 					partitionKeyLength: 0
 				},
+				mem: "16GiB",
+				cpu: 2,
 				name: "byCloneKeyBySample",
 				path: ["tsv"]
 			} ]
@@ -423,6 +425,8 @@ self.body(func(inputs) {
 					storageFormat: "Binary",
 					partitionKeyLength: 0
 				},
+				mem: "24GiB",
+				cpu: 2,
 				name: "byCloneKey",
 				path: ["tsv"]
 			} ]
@@ -491,6 +495,8 @@ self.body(func(inputs) {
 					storageFormat: "Binary",
 					partitionKeyLength: 1
 				},
+				mem: "16GiB",
+				cpu: 2,
 				name: "abundanceTable",
 				path: ["abundanceTsv"]
 			}, {
@@ -501,6 +507,8 @@ self.body(func(inputs) {
 					columns: columnsSpecPerClonotypeSc,
 					storageFormat: "Binary"
 				},
+				mem: "12GiB",
+				cpu: 2,
 				name: "aggregates",
 				path: ["clonotypeTsv"]
 			} ]
@@ -569,6 +577,8 @@ self.body(func(inputs) {
 							storageFormat: "Binary",
 							partitionKeyLength: 0
 						},
+						mem: "24GiB",
+						cpu: 2,
 						name: propertiesTableName,
 						path: [ propertiesTsvOutputName ]
 					} ]