@platforma-open/milaboratories.mixcr-shm-trees.workflow 4.0.1 → 4.2.0

package/.turbo/turbo-build.log

@@ -1,7 +1,7 @@
  WARN  Issue while reading "/home/runner/work/mixcr-shm-trees/mixcr-shm-trees/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-shm-trees.workflow@4.0.1 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
-> rm -rf dist && pl-tengo check && pl-tengo build
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@4.2.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> shx rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/export-settings.lib.tengo"...
 Processing "src/main.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 4.2.0
+
+### Minor Changes
+
+- f16a929: Add ability to control CPU and MEM allocated for each sample processing via advanced settings of a block
+
+## 4.1.0
+
+### Minor Changes
+
+- 2ce3a8a: SDK version update
+
 ## 4.0.1
 
 ### Patch Changes

package/package.json

@@ -1,25 +1,25 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "4.0.1",
+  "version": "4.2.0",
   "type": "module",
   "description": "Tengo-based template",
   "//": {
-    "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
+    "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && shx rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
   },
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.3.3"
+    "@platforma-sdk/workflow-tengo": "^5.5.9"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.3.0",
+    "@platforma-sdk/tengo-builder": "^2.3.3",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-235-develop",
     "@platforma-open/milaboratories.software-mitool": "2.3.1-24-main",
     "@platforma-open/milaboratories.software-ptransform": "^1.6.6",
-    "@platforma-sdk/test": "^1.44.7",
+    "@platforma-sdk/test": "^1.45.11",
     "vitest": "~2.1.8",
     "typescript": "~5.5.4"
   },
   "scripts": {
-    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",
     "format": "/usr/bin/env emacs --script ./format.el"
   }
 }

package/src/main.tpl.tengo

@@ -46,7 +46,9 @@ wf.body(func(args) {
 		},
 		params: {
 			downsampling: args.downsampling,
-			sequencesOfInterest: args.sequencesOfInterest
+			sequencesOfInterest: args.sequencesOfInterest,
+			perProcessMemGB: args.perProcessMemGB,
+			perProcessCPUs: args.perProcessCPUs
 		}
 	})
 

package/src/mixcr-export.tpl.tengo

@@ -32,6 +32,9 @@ self.body(func(inputs) {
 	shmTreeNodesWithClonesEnsureUniquenessParams := params.shmTreeNodesWithClonesEnsureUniquenessParams
 	shmTreeNodesUniqueIsotypeEnsureUniquenessParams := params.shmTreeNodesUniqueIsotypeEnsureUniquenessParams
 
+    perProcessMemGB := inputs.perProcessMemGB
+    perProcessCPUs := inputs.perProcessCPUs
+
     addLibraryFile := func(cmdBuilder) {
         if !is_undefined(library) {
             if libraryFormat == "repseqio.json.gz" {
@@ -79,6 +82,16 @@ self.body(func(inputs) {
         arg("exportShmTreesWithNodes").
         env("CIDADHOC", "1234")
 
+    // CPUs number per process
+    if !is_undefined(perProcessCPUs) && perProcessCPUs > 0 {
+        shmTreeNodesExportsCmdBuilder.cpu(perProcessCPUs)
+    }
+
+    // Memory limit per process
+    if !is_undefined(perProcessMemGB) && perProcessMemGB > 0 {
+        shmTreeNodesExportsCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+    }
+
     addLibraryFile(shmTreeNodesExportsCmdBuilder)
 
     for arg in shmTreeNodesArgs {
@@ -108,6 +121,16 @@ self.body(func(inputs) {
         arg("--only-observed").
         env("CIDADHOC", "1234")
 
+    // CPUs number per process
+    if !is_undefined(perProcessCPUs) && perProcessCPUs > 0 {
+        shmTreeNodesWithClonesExportsCmdBuilder.cpu(perProcessCPUs)
+    }
+
+    // Memory limit per process
+    if !is_undefined(perProcessMemGB) && perProcessMemGB > 0 {
+        shmTreeNodesWithClonesExportsCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+    }
+
     addLibraryFile(shmTreeNodesWithClonesExportsCmdBuilder)
 
     for arg in shmTreeNodesWithClonesArgs {

package/src/mixcr-shm-trees.tpl.tengo

@@ -33,6 +33,9 @@ self.body(func(inputs) {
     libraryFormat := globalParams.libraryFormat
     downsampling := globalParams.downsampling
 
+    perProcessMemGB := inputs.perProcessMemGB
+    perProcessCPUs := inputs.perProcessCPUs
+
     ll.assert(!is_undefined(datasetTypes), "datasetTypes undefined")
 
     addLibraryFile := func(cmdBuilder) {
@@ -66,6 +69,16 @@ self.body(func(inputs) {
         arg("--output-template").arg("alleles/{file_name}.clns").
         env("CIDADHOC", "1234")
 
+    // CPUs number per process
+    if !is_undefined(perProcessCPUs) && perProcessCPUs > 0 {
+        allelesCmdBuilder.cpu(perProcessCPUs)
+    }
+
+    // Memory limit per process
+    if !is_undefined(perProcessMemGB) && perProcessMemGB > 0 {
+        allelesCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+    }
+
     addLibraryFile(allelesCmdBuilder)
 
     if !is_undefined(globalParams.seed) {
@@ -136,6 +149,17 @@ self.body(func(inputs) {
                     addFile("clones.clns", entry.afterAlleles).
                     saveFile("clones.downsampled.clns").
                     env("CIDADHOC", "1234")
+
+                // CPUs number per process
+                if !is_undefined(perProcessCPUs) && perProcessCPUs > 0 {
+                    downsamplingCmdBuilder.cpu(perProcessCPUs)
+                }
+
+                // Memory limit per process
+                if !is_undefined(perProcessMemGB) && perProcessMemGB > 0 {
+                    downsamplingCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+                }
+
                 addLibraryFile(downsamplingCmdBuilder)
                 downsamplingCmd := downsamplingCmdBuilder.run()
 
@@ -161,6 +185,16 @@ self.body(func(inputs) {
         saveFile("report.json").
         env("CIDADHOC", "1234")
 
+    // CPUs number per process
+    if !is_undefined(perProcessCPUs) && perProcessCPUs > 0 {
+        shmTreesCmdBuilder.cpu(perProcessCPUs)
+    }
+
+    // Memory limit per process
+    if !is_undefined(perProcessMemGB) && perProcessMemGB > 0 {
+        shmTreesCmdBuilder.mem(string(perProcessMemGB) + "GiB")
+    }
+
     if !is_undefined(globalParams.seed) {
         shmTreesCmdBuilder.env("SEED", globalParams.seed)
     }

package/src/process.tpl.tengo

@@ -9,6 +9,7 @@ xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 smart := import("@platforma-sdk/workflow-tengo:smart")
 text := import("text")
 json := import("json")
+times := import("times")
 exportSettings := import(":export-settings")
 prepareDonorColumn := import(":prepare-donor-column")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
@@ -41,7 +42,7 @@ soiTpl := assets.importTemplate(":soi")
 
 self.body(func(inputs) {
 	// overall description of data that we have.
-    dataDescription := {
+	dataDescription := {
 		hasUmiTags: false,
 		hasCellTags: false,
 		// will be filled
@@ -50,6 +51,12 @@ self.body(func(inputs) {
 		cellsAssembled: false
 	}
 
+	perProcessMemGB := inputs.params.perProcessMemGB
+	perProcessCPUs := inputs.params.perProcessCPUs
+	inputParams := inputs.params
+	delete(inputParams, "perProcessMemGB") // do not affect deduplication of results
+	delete(inputParams, "perProcessCPUs") // do not affect deduplication of results
+
 	blockId := inputs.etc.blockId
 	firstDatasetSpec := inputs.etc.firstDatasetSpec
 
@@ -173,10 +180,15 @@ self.body(func(inputs) {
 			traceSteps: [{type: "milaboratories.mixcr-shm-trees", id: blockId, importance: 19, label: "SHM Trees"}],
 			extra: {
 				library: is_undefined(library) ? smart.createNullResource() : library.data,
-				globalParams: maps.merge(inputs.params, {
+				globalParams: maps.merge(inputParams, {
+					seed: times.time_string(times.now()),
 					datasetTypes: datasetTypes,
 					libraryFormat: libraryFormat
 				})
+			},
+			metaExtra: {
+				perProcessMemGB: perProcessMemGB,
+				perProcessCPUs: perProcessCPUs
 			}
 		}
 	)
@@ -225,6 +237,10 @@ self.body(func(inputs) {
 					shmTreeNodesWithClonesEnsureUniquenessParams: tablesAggregation.ensureUniquenessParamsFromPconvParams(shmTreeNodesWithClonesTableOptions.pfconvParams),
 					shmTreeNodesUniqueIsotypeEnsureUniquenessParams: tablesAggregation.ensureUniquenessParamsFromPconvParams(shmTreeNodesUniqueIsotypeTableOptions.pfconvParams)
 				}
+			},
+			metaExtra: {
+				perProcessMemGB: perProcessMemGB,
+				perProcessCPUs: perProcessCPUs
 			}
 		}
 	)