@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.5 → 1.21.7

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.5 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.7 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.21.7
+
+### Patch Changes
+
+- b67eb61: Upgrade MiXCR to 4.7.0-343-develop — packed NucleotideSequence storage for 4x memory reduction
+
+## 1.21.6
+
+### Patch Changes
+
+- a463f4f: Fix memory allocation for aggregation step and correct GB/GiB unit mismatch across all workflow templates
+
 ## 1.21.5
 
 ### Patch Changes

package/package.json

@@ -1,11 +1,11 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.21.5",
+  "version": "1.21.7",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.11.0",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-317-develop",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-343-develop",
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {

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

@@ -31,9 +31,18 @@ self.body(func(inputs) {
 	inputMap := inputData.inputs()
 	numberOfSamples := len(inputMap)
 
+	baseMemGB := 32
+	if !is_undefined(inputs.perProcessMemGB) {
+		baseMemGB = inputs.perProcessMemGB / 2
+	}
+
+	perSampleMem := int(math.max(2, baseMemGB / 10))
+	effectiveSamples := int(math.max(numberOfSamples, 3))
+	memGB := int(math.min(312, math.max(baseMemGB * 3 / 2, effectiveSamples * perSampleMem)))
+
 	wf := pt.workflow().
 		inMediumQueue().
-		mem(int(math.max(numberOfSamples, 64)) * units.GB).
+		mem(memGB * units.GiB).
 		cpu(int(math.max(numberOfSamples, 32)))
 
 	dataFrames := []

package/src/export-report.tpl.tengo

@@ -204,7 +204,7 @@ self.body(func(inputs) {
 		baseMemGB = perProcessMemGB
 	}
 	memGB := func(floorGB, divisor) {
-		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GB"
+		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GiB"
 	}
 
 	// Count clonotypes filtered by stop codons and out-of-frame per sample

package/src/mixcr-analyze.tpl.tengo

@@ -143,9 +143,9 @@ self.body(func(inputs) {
 	// Memory limit per process
     if !is_undefined(perProcessMemGB) {
         // memory per process was set in "Advanced Settings" block directly
-		mixcrCmdBuilder.mem(string(perProcessMemGB) + "GB")
+		mixcrCmdBuilder.mem(string(perProcessMemGB) + "GiB")
 	} else {
-		mixcrCmdBuilder.mem("64GB")
+		mixcrCmdBuilder.mem("64GiB")
 	}
 
 	if !is_undefined(limitInput) {

package/src/mixcr-export.tpl.tengo

@@ -179,11 +179,11 @@ self.body(func(inputs) {
 
 	// Memory for downstream operations, linked to user override with hardcoded floors
 	baseMemGB := 64
-	if !is_undefined(params.perProcessMemGB) {
-		baseMemGB = params.perProcessMemGB
+	if !is_undefined(inputs.perProcessMemGB) {
+		baseMemGB = inputs.perProcessMemGB
 	}
 	memGB := func(floorGB, divisor) {
-		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GB"
+		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GiB"
 	}
 
 	hashKeyDerivationExpressionPt := func(sourceColumns) {

package/src/process.tpl.tengo

@@ -77,9 +77,9 @@ self.body(func(inputs) {
 	if !is_undefined(perProcessMemGB) {
 		baseMemGB = perProcessMemGB
 	}
-	// Returns max(floor, baseMemGB / divisor) as a string like "32GB"
+	// Returns max(floor, baseMemGB / divisor) as a string like "32GiB"
 	memGB := func(floorGB, divisor) {
-		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GB"
+		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GiB"
 	}
 
 	fileExtension := inputSpec.domain["pl7.app/fileExtension"]
@@ -285,9 +285,11 @@ self.body(func(inputs) {
 					cdr3SeqColumns: cdr3SeqColumns,
 					stopCodonTypes: params.stopCodonTypes,
 					stopCodonReplacements: params.stopCodonReplacements,
-					perProcessMemGB: perProcessMemGB,
 					isLibraryFileGzipped: params.isLibraryFileGzipped
 				}, { removeUndefs: true })
+			},
+			metaExtra: {
+				perProcessMemGB: perProcessMemGB
 			}
 		}
 	)
@@ -339,6 +341,9 @@ self.body(func(inputs) {
 					schemaPerClonotypeAggregates: columnsToSchema(columnsSpecPerClonotypeAggregates),
 					schemaPerSample: columnsToSchema(columnsSpecPerSample)
 				}
+			},
+			metaExtra: {
+				perProcessMemGB: perProcessMemGB
 			}
 		}
 	)