@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.2 → 1.21.4

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@1.21.2 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.4 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
 
+## 1.21.4
+
+### Patch Changes
+
+- b93d463: fix memory for export
+
+## 1.21.3
+
+### Patch Changes
+
+- 637e770: fix memory for export
+
 ## 1.21.2
 
 ### Patch Changes

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.21.2",
+  "version": "1.21.4",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.10.1",
+    "@platforma-sdk/workflow-tengo": "5.11.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-317-develop",
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.30"
+    "@platforma-sdk/tengo-builder": "2.5.1"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/export-report.tpl.tengo

@@ -13,6 +13,7 @@ pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 qcReportColumns := import(":qc-report-columns")
 
+math := import("math")
 json := import("json")
 
 self.defineOutputs("qcReportTable")
@@ -23,6 +24,7 @@ ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptab
 
 self.body(func(inputs) {
     clnsData := inputs.clnsData
+	perProcessMemGB := inputs.perProcessMemGB
     presetSpecForBack := inputs.presetSpecForBack
     sampleIdAxisSpec := inputs.sampleIdAxisSpec
     chains := inputs.chains
@@ -196,6 +198,15 @@ self.body(func(inputs) {
     // Join counts and overwrite totalClonotypes to reflect exported (productive) clones
     joinedDf := processedDf.join(aggregatedCounts, { how: "left", on: ["sampleId"] })
 
+    // Memory for downstream operations, linked to user override with hardcoded floors
+	baseMemGB := 64
+	if !is_undefined(perProcessMemGB) {
+		baseMemGB = perProcessMemGB
+	}
+	memGB := func(floorGB, divisor) {
+		return string(int(math.max(floorGB, baseMemGB / divisor))) + "GB"
+	}
+
 	// Count clonotypes filtered by stop codons and out-of-frame per sample
 	filterCountDfs := []
 	mixcrChainsArg := text.join(chainsForMixcr, ",")
@@ -203,7 +214,7 @@ self.body(func(inputs) {
 		sampleId := json.decode(key)[0]
 		exportFiltersCmd := exec.builder().
 			inMediumQueue().
-			mem("16GiB").
+			mem(memGB(16, 3)).
 			cpu(2).
 			software(mixcrSw).
 			env("MI_USE_SYSTEM_CA", "true").

package/src/mixcr-export.tpl.tengo

@@ -196,7 +196,7 @@ self.body(func(inputs) {
 	createExport := func(additionalAction) {
 		mixcrCmdBuilder := exec.builder().
 			inMediumQueue().
-			mem(memGB(12, 2)).
+			mem(memGB(16, 3)).
 		    cpu(2).
 			printErrStreamToStdout().
 			software(mixcrSw).

package/src/process.tpl.tengo

@@ -357,6 +357,7 @@ self.body(func(inputs) {
 		clonotypeTablesData: clonotypeTablesData,
 		hasUmi: hasUMI,
 		umiTags: umiTags,
+		perProcessMemGB: perProcessMemGB,
 		productiveFeature: productiveFeature,
 		stopCodonTypes: params.stopCodonTypes,
 		stopCodonReplacements: params.stopCodonReplacements