@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.19.3 → 2.20.0

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@2.19.3 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.20.0 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
 
+## 2.20.0
+
+### Minor Changes
+
+- CPU and Memory requests for all jobs
+
+## 2.19.4
+
+### Patch Changes
+
+- da76979: MiXCR Software upgrade, export memory increase
+
 ## 2.19.3
 
 ### Patch Changes

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.19.3",
+  "version": "2.20.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.7.4",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-169-develop"
+    "@platforma-sdk/workflow-tengo": "^4.8.0",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-178-develop"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.10",
-    "@platforma-sdk/test": "^1.34.3",
+    "@platforma-sdk/test": "^1.34.6",
     "vitest": "~2.1.9",
     "typescript": "~5.5.4"
   },

package/src/calculate-preset-info.tpl.tengo

@@ -15,7 +15,7 @@ self.validateInputs({
 	}
 })
 
-mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:low-memory")
+mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:memory-from-limits")
 
 self.defineOutputs("preset", "presetSpecForBack")
 
@@ -25,6 +25,7 @@ self.body(func(inputs) {
 
 	mixcrExportPresetCmdBuilder := exec.builder().
 		inUiQueue().
+		mem("200MiB").
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").
 		printErrStreamToStdout().
@@ -55,6 +56,7 @@ self.body(func(inputs) {
 
 	mixcrForBackCmd := exec.builder().
 		inUiQueue().
+		mem("200MiB").
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").
 		printErrStreamToStdout().

package/src/list-presets.tpl.tengo

@@ -5,14 +5,18 @@ ll := import("@platforma-sdk/workflow-tengo:ll")
 exec := import("@platforma-sdk/workflow-tengo:exec")
 file := import("@platforma-sdk/workflow-tengo:file")
 assets := import("@platforma-sdk/workflow-tengo:assets")
+feats := import("@platforma-sdk/workflow-tengo:feats")
 
 self.defineOutputs("presets")
 
-mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:low-memory")
+mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:memory-from-limits")
 
 self.body(func(inputs) {
+	// ll.print("__THE_LOG__ feats.computeLimits " + feats.computeLimits)
+	ll.print("__THE_LOG__ asdhjkajsdjasdjk")
 	listPresets := exec.builder().
-		inUiQueue().
+		inMediumQueue().
+		mem("202MiB").
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").
 		arg("listPresetSpecificationsForUI").

package/src/mixcr-analyze.tpl.tengo

@@ -16,7 +16,7 @@ json := import("json")
 
 self.defineOutputs("qc", "reports", "log", "clns")
 
-mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:main")
+mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:memory-from-limits")
 
 progressPrefix := "[==PROGRESS==]"
 
@@ -64,11 +64,17 @@ self.body(func(inputs) {
 		printErrStreamToStdout().
 		env("MI_PROGRESS_PREFIX", progressPrefix).
 		software(mixcrSw).
-		mem("64GiB").
 		cpu(32).
 		secret("MI_LICENSE", "MI_LICENSE").
 		arg("analyze")
 
+	if hasAssembleContigs || hasAssembleCells {
+		// allow to use more memory for single cell analysis
+		mixcrCmdBuilder.mem("128GiB")
+	} else {
+		mixcrCmdBuilder.mem("64GiB")
+	}
+
 	if !is_undefined(limitInput) {
 		mixcrCmdBuilder.arg("--limit-input").arg(string(limitInput))
 	}

package/src/mixcr-export.tpl.tengo

@@ -11,8 +11,7 @@ json := import("json")
 
 self.defineOutputs("tsv", "tsvForSingleCell")
 
-mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:low-memory")
-ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptabler:main")
+mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:memory-from-limits")
 
 self.body(func(inputs) {
 	clnsFile := inputs[pConstants.VALUE_FIELD_NAME]
@@ -43,7 +42,7 @@ self.body(func(inputs) {
 	createExport := func(additionalAction) {
 		mixcrCmdBuilder := exec.builder().
 			inMediumQueue().
-			ram("6GiB").
+			ram("12GiB").
 		    cpu(2).
 			printErrStreamToStdout().
 			dontSaveStdoutOrStderr().
@@ -96,7 +95,7 @@ self.body(func(inputs) {
 	// PTabler processing for main TSV output
 	wfMain := pt.workflow().
 		inMediumQueue().
-		mem("4GiB").
+		mem("8GiB").
 		cpu(2)
 
 	frameInputMap := {
@@ -136,7 +135,7 @@ self.body(func(inputs) {
 		// PTabler processing for single-cell TSV output
 		wfSingleCell := pt.workflow().
 			inMediumQueue().
-			mem("2GiB").
+			mem("4GiB").
 			cpu(2)
 
 		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, { xsvType: "tsv", inferSchema: false })