@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.10 → 1.21.12

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@1.21.10 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.12 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 +1,17 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.21.12
+
+### Patch Changes
+
+- 2bd5020: Fixed bug in QC table when using FR1:FR4 assembling feature. SDK Update
+
+## 1.21.11
+
+### Patch Changes
+
+- a44cc33: Add an option to disable low-quality read mapping
+
 ## 1.21.10
 
 ### Patch Changes

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

@@ -169,13 +169,27 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
+	if assemblingFeature == "FR1:FR4" {
+		productiveFeature = "VDJRegion"
+	}
+
+
+
+
+
+
 
 	outputProductiveFeature := productiveFeature
 	if assemblingFeature != "VDJRegion" && assemblingFeature != "CDR3" {
 		parts := text.split(assemblingFeature, ":")
 		if len(parts) == 2 && parts[1] == "FR4" {
+			if parts[0] == "FR1" {
 
-			outputProductiveFeature = parts[0] + "_TO_FR4"
+				outputProductiveFeature = "VDJRegion"
+			} else {
+
+				outputProductiveFeature = parts[0] + "_TO_FR4"
+			}
 		}
 	}
 	

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.21.10",
+  "version": "1.21.12",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.11.0",
+    "@platforma-sdk/workflow-tengo": "6.3.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-347-develop",
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.5.1"
+    "@platforma-sdk/tengo-builder": "4.0.5"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

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

@@ -165,17 +165,31 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	productiveFeature := formatAssemblingFeature(assemblingFeature)
 
+	// FR1:FR4 spans the entire VDJRegion; MiXCR canonicalizes {FR1Begin:FR4End} to the
+	// "VDJRegion" name in every exported column (isProductiveVDJRegion, isOOFVDJRegion,
+	// nSeqVDJRegion, ...). Normalize here so the export args we pass and the column names
+	// we (and export-report.tpl) expect both agree with MiXCR's output.
+	if assemblingFeature == "FR1:FR4" {
+		productiveFeature = "VDJRegion"
+	}
+
 	// MiXCR column naming for range features:
-	// - Ranges ending at FR4 have named aliases: CDR1_TO_FR4, FR2_TO_FR4, CDR2_TO_FR4, FR3_TO_FR4
-	//   (defined in repseqio GeneFeature.java)
+	// - FR1:FR4 is the full VDJRegion; MiXCR names it "VDJRegion", NOT "FR1_TO_FR4"
+	//   (FR1Begin:FR4End is the canonical VDJRegion in repseqio GeneFeature.java)
+	// - Other ranges ending at FR4 have named aliases: CDR1_TO_FR4, FR2_TO_FR4, CDR2_TO_FR4, FR3_TO_FR4
 	// - All other ranges use {XBegin:YEnd} format (e.g. {CDR1Begin:CDR3End})
 	// - Simple features (CDR3, VDJRegion) use their name directly
 	outputProductiveFeature := productiveFeature
 	if assemblingFeature != "VDJRegion" && assemblingFeature != "CDR3" {
 		parts := text.split(assemblingFeature, ":")
 		if len(parts) == 2 && parts[1] == "FR4" {
-			// MiXCR has a named alias for this range
-			outputProductiveFeature = parts[0] + "_TO_FR4"
+			if parts[0] == "FR1" {
+				// Full range: MiXCR uses the canonical "VDJRegion" name, not "FR1_TO_FR4"
+				outputProductiveFeature = "VDJRegion"
+			} else {
+				// MiXCR has a named alias for this range
+				outputProductiveFeature = parts[0] + "_TO_FR4"
+			}
 		}
 	}
 	

package/src/main.tpl.tengo

@@ -144,6 +144,7 @@ wf.body(func(args) {
 			assemblingFeature: args.assemblingFeature,
 			imputeGermline: args.imputeGermline,
 			badQualityThreshold: args.badQualityThreshold,
+			disableLowQualityMapping: args.disableLowQualityMapping,
 			isLibraryFileGzipped: isLibraryFileGzipped,
 			stopCodonTypes: args.stopCodonTypes,
 			stopCodonReplacements: args.stopCodonReplacements

package/src/mixcr-analyze.tpl.tengo

@@ -122,6 +122,12 @@ self.body(func(inputs) {
 		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.minimalQuality=" + string(int(badQualityThreshold)))
 	}
 
+	// Disable the deferred-reads mapping phase
+	disableLowQualityMapping := params.disableLowQualityMapping
+	if !is_undefined(disableLowQualityMapping) && disableLowQualityMapping {
+		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.maxBadPointsPercent=0")
+	}
+
 		// if (!is_undefined(threePrimePrimer)) {
 		// 	mixcrCmdBuilder.arg("--floating-left-alignment-boundary")
 		// } else {

package/src/process.tpl.tengo

@@ -221,6 +221,7 @@ self.body(func(inputs) {
 					assemblingFeature: params.assemblingFeature,
 					imputeGermline: params.imputeGermline,
 					badQualityThreshold: params.badQualityThreshold,
+					disableLowQualityMapping: params.disableLowQualityMapping,
 					isLibraryFileGzipped: params.isLibraryFileGzipped
 				}, { removeUndefs: true }),
 				limitInput: limitInput