@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.18.1 → 1.19.0

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@1.18.1 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.19.0 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 +1,11 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.19.0
+
+### Minor Changes
+
+- b6a7c08: Add assembly quality threshold setting to advanced options, allowing users to control the base quality cutoff for clonotype seeding during assembly (MiXCR badQualityThreshold parameter)
+
 ## 1.18.1
 
 ### Patch Changes

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.18.1",
+  "version": "1.19.0",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {

package/src/main.tpl.tengo

@@ -60,7 +60,7 @@ wf.body(func(args) {
 		limitInput: limitInput,
 		cdr3Sequences: args.cdr3Sequences,
 
-		params: smart.createJsonResource({
+		params: smart.createJsonResource(maps.clone({
 			blockId: blockId,
 			perProcessMemGB: perProcessMemGB,
 			perProcessCPUs: perProcessCPUs,
@@ -69,9 +69,10 @@ wf.body(func(args) {
 			cloneClusteringMode: cloneClusteringMode,
 			tagPattern: args.tagPattern,
 			assemblingFeature: args.assemblingFeature,
+			badQualityThreshold: args.badQualityThreshold,
 			stopCodonTypes: args.stopCodonTypes,
 			stopCodonReplacements: args.stopCodonReplacements
-		})
+		}, { removeUndefs: true }))
 	})
 
 	exports := {

package/src/mixcr-analyze.tpl.tengo

@@ -91,6 +91,12 @@ self.body(func(inputs) {
 		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters=null")
 	}
 
+	// Assembly quality threshold
+	badQualityThreshold := params.badQualityThreshold
+	if !is_undefined(badQualityThreshold) {
+		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.badQualityThreshold=" + string(int(badQualityThreshold)))
+	}
+
 		// if (!is_undefined(threePrimePrimer)) {
 		// 	mixcrCmdBuilder.arg("--floating-left-alignment-boundary")
 		// } else {

package/src/process.tpl.tengo

@@ -201,14 +201,15 @@ self.body(func(inputs) {
 			traceSteps: [{type: "milaboratories.mixcr-amplicon-alignment", id: blockId, importance: 20, label: "MiXCR generic amplicon"}],
 
 			extra: {
-				params: {
+				params: maps.clone({
 					fileExtension: fileExtension,
 					referenceLibrary: referenceLibrary,
 					cloneClusteringMode: cloneClusteringMode,
 					hasUMI: hasUMI,
 					tagPattern: tagPattern,
-					assemblingFeature: params.assemblingFeature
-				},
+					assemblingFeature: params.assemblingFeature,
+					badQualityThreshold: params.badQualityThreshold
+				}, { removeUndefs: true }),
 				limitInput: limitInput
 			},