@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.13.0 → 3.15.0

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@3.13.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.15.0 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
 
+## 3.15.0
+
+### Minor Changes
+
+- 224eef5: clonotypeKey now includes cHit instead of cGene in splitByC case
+
+## 3.14.0
+
+### Minor Changes
+
+- 4fcd94b: relaxed mixcr assemble parameters for high diversity datasets
+
 ## 3.13.0
 
 ### Minor Changes

package/dist/tengo/lib/calculate-export-specs.lib.tengo

@@ -174,8 +174,8 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 			[ "-jGene" ]
 		]
 		if splitByC {
-			clonotypeKeyColumns += ["bestCGene"]
-			clonotypeKeyArgs += [ [ "-cGene" ] ]
+			clonotypeKeyColumns += ["bestCHit"]
+			clonotypeKeyArgs += [ [ "-cHit" ] ]
 		}
 	}
 

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.13.0",
+  "version": "3.15.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.5.9",
+    "@platforma-sdk/workflow-tengo": "^5.5.15",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-233-develop"
   },
   "devDependencies": {
     "@milaboratories/ts-configs": "^1.0.6",
     "@platforma-sdk/tengo-builder": "^2.3.3",
-    "@platforma-sdk/test": "^1.45.9",
+    "@platforma-sdk/test": "^1.45.20",
     "vitest": "~2.1.9",
     "typescript": "~5.6.3"
   },

package/src/calculate-export-specs.lib.tengo

@@ -174,8 +174,8 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 			[ "-jGene" ]
 		]
 		if splitByC {
-			clonotypeKeyColumns += ["bestCGene"]
-			clonotypeKeyArgs += [ [ "-cGene" ] ]
+			clonotypeKeyColumns += ["bestCHit"]
+			clonotypeKeyArgs += [ [ "-cHit" ] ]
 		}
 	}
 

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

@@ -29,7 +29,6 @@ self.body(func(inputs) {
 		software(mixcrSw).
 		env("MI_USE_SYSTEM_CA", "true").
 		secret("MI_LICENSE", "MI_LICENSE").
-		printErrStreamToStdout().
 		arg("exportPreset")
 
 	if smart.isResource(preset) /* file */ {
@@ -61,7 +60,6 @@ self.body(func(inputs) {
 		software(mixcrSw).
 		env("MI_USE_SYSTEM_CA", "true").
 		secret("MI_LICENSE", "MI_LICENSE").
-		printErrStreamToStdout().
 		arg("presetSpecificationsForBack").
 		addFile("preset.yaml", mixcrExportPresetCmd.getFile("preset.json")).
 		arg("preset.yaml").

package/src/main.tpl.tengo

@@ -117,6 +117,7 @@ wf.body(func(args) {
 			limitInput: limitInput,
 			perProcessMemGB: perProcessMemGB,
 			perProcessCPUs: perProcessCPUs,
+				highDiversityLibrary: args.highDiversityLibrary,
 			blockId: blockId,
 			libraryId: libraryId,
 			presetCommonName: args.presetCommonName,

package/src/mixcr-analyze.tpl.tengo

@@ -66,6 +66,7 @@ self.body(func(inputs) {
 
 	mixcrCmdBuilder := exec.builder().
 		printErrStreamToStdout().
+		saveStdoutStream().
 		env("MI_USE_SYSTEM_CA", "true").
 		env("MI_PROGRESS_PREFIX", progressPrefix).
 		software(mixcrSw).
@@ -121,6 +122,16 @@ self.body(func(inputs) {
 			arg(preset.name)
 	}
 
+	// High diversity library tuning
+	highDiversityLibrary := params.highDiversityLibrary
+	if !is_undefined(highDiversityLibrary) && highDiversityLibrary {
+		mixcrCmdBuilder.
+			arg("-Massemble.cloneAssemblerParameters.minimalQuality=20").
+			arg("-Massemble.cloneAssemblerParameters.badQualityThreshold=10").
+			arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchParameters=oneMismatchOrIndel").
+			arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchDepth=1")
+	}
+
 	inputMap := inputData.inputs()
 	if inputDataMeta.keyLength == 0 {
 		ll.assert(aggregationAxesNames == [], "unexpected aggregation axes names")

package/src/mixcr-export.tpl.tengo

@@ -66,8 +66,6 @@ self.body(func(inputs) {
 			inMediumQueue().
 			mem(string(exportMemGB) + "GiB").
 		    cpu(2).
-			printErrStreamToStdout().
-			dontSaveStdoutOrStderr().
 			env("MI_USE_SYSTEM_CA", "true").
 			software(mixcrSw).
 			secret("MI_LICENSE", "MI_LICENSE").

package/src/process.tpl.tengo

@@ -267,7 +267,8 @@ self.body(func(inputs) {
 					limitInput: limitInput,
 					fileExtension: fileExtension,
 					reports: reports,
-					isLibraryFileGzipped: isLibraryFileGzipped
+					isLibraryFileGzipped: isLibraryFileGzipped,
+					highDiversityLibrary: params.highDiversityLibrary
 				},
 				library: library,
 				presetContent: presetContent