@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.21.2 → 2.23.0

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@2.21.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.23.0 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
 
+## 2.23.0
+
+### Minor Changes
+
+- e152a2f: SDK Upgrade: fix for compatibility issues with old platformas and final migration to request-based task scheduling
+
+## 2.22.0
+
+### Minor Changes
+
+- a65fef4: Custom settings for memory and CPU count added
+
 ## 2.21.2
 
 ### Patch Changes

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.21.2",
+  "version": "2.23.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.9.1",
+    "@platforma-sdk/workflow-tengo": "^4.9.2",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-190-develop"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.11",
-    "@platforma-sdk/test": "^1.37.8",
+    "@platforma-sdk/test": "^1.37.16",
     "vitest": "~2.1.9",
     "typescript": "~5.5.4"
   },

package/src/list-presets.tpl.tengo

@@ -14,6 +14,7 @@ mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:
 self.body(func(inputs) {
 	listPresets := exec.builder().
 		inUiQueue().
+		cpu(1).
 		mem("512MiB").
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").

package/src/main.tpl.tengo

@@ -56,6 +56,8 @@ wf.body(func(args) {
 	}
 
 	limitInput := args.limitInput
+	perProcessMemGB := args.perProcessMemGB
+	perProcessCPUs := args.perProcessCPUs
 	isLibraryFileGzipped := false
 
 	library := false
@@ -112,6 +114,8 @@ wf.body(func(args) {
 			species: species,
 			receptorsOrChains: receptorsOrChains,
 			limitInput: limitInput,
+			perProcessMemGB: perProcessMemGB,
+			perProcessCPUs: perProcessCPUs,
 			blockId: blockId,
 			libraryId: libraryId,
 			presetCommonName: args.presetCommonName,

package/src/mixcr-analyze.tpl.tengo

@@ -31,6 +31,8 @@ self.body(func(inputs) {
 	params := inputs.params
 	species := params.species
 	limitInput := params.limitInput
+	perProcessMemGB := inputs.perProcessMemGB
+	perProcessCPUs := inputs.perProcessCPUs
 	fileExtension := params.fileExtension
 	reports := params.reports
 	isLibraryFileGzipped := params.isLibraryFileGzipped
@@ -68,11 +70,21 @@ self.body(func(inputs) {
 		printErrStreamToStdout().
 		env("MI_PROGRESS_PREFIX", progressPrefix).
 		software(mixcrSw).
-		cpu(16).
 		secret("MI_LICENSE", "MI_LICENSE").
 		arg("analyze").arg("--use-local-temp")
 
-	if hasMiToolSteps {
+	// CPUs number per process
+	if !is_undefined(perProcessCPUs) {
+	    mixcrCmdBuilder.cpu(perProcessCPUs)
+	} else {
+	    mixcrCmdBuilder.cpu(16)     // default CPUs number per sample
+	}
+
+	// Memory limit per process
+    if !is_undefined(perProcessMemGB) {
+        // memory per process was set in "Advanced Settings" block directly
+		mixcrCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+	} else if hasMiToolSteps {
 		// allow to use more memory for single cell analysis with mitool pre-
 		mixcrCmdBuilder.mem("192GiB")
 	} else if hasAssembleContigs || hasAssembleCells {

package/src/process.tpl.tengo

@@ -62,6 +62,8 @@ self.body(func(inputs) {
 	// can be either receptors or chains
 	receptorsOrChains := params.receptorsOrChains
 	limitInput := params.limitInput
+	perProcessMemGB := params.perProcessMemGB
+	perProcessCPUs := params.perProcessCPUs
 	blockId := params.blockId
 	libraryId := params.libraryId
 	presetCommonName := params.presetCommonName
@@ -262,7 +264,11 @@ self.body(func(inputs) {
 				},
 				library: library,
 				presetContent: presetContent
-			}
+			},
+            metaExtra: {
+                perProcessMemGB: perProcessMemGB,
+                perProcessCPUs: perProcessCPUs
+            }
 		}
 	)