@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.17.1 → 3.18.0

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@3.17.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.18.0 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 +1,11 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 3.18.0
+
+### Minor Changes
+
+- 070fc0b: Min quality checkbox, refactored error correction, dep updates
+
 ## 3.17.1
 
 ### Patch Changes

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

@@ -129,13 +129,18 @@ addSpec := func(columns, additionalSpec) {
 
 
 
-calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
+calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, exportMinQuality) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
+	
+
+	if is_undefined(exportMinQuality) {
+		exportMinQuality = false
+	}
 
 	isSingleCell := !is_undefined(cellTags) && len(cellTags) > 0
 	hashCellKey := isSingleCell && len(cellTags) > 1
@@ -482,7 +487,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
-				if !isImputed && !isAminoAcid {
+				if !isImputed && !isAminoAcid && exportMinQuality {
 					columnsSpecPerClonotypeNoAggregates += [ {
 							column: "minQual" + featureU,
 							id: "min-qual-" + featureL,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.17.1",
+  "version": "3.18.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^5.6.6",

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

@@ -129,13 +129,18 @@ addSpec := func(columns, additionalSpec) {
 // Ordering rules
 //   AA Sequences
 
-calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
+calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, exportMinQuality) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
+	
+	// Default to false if not provided
+	if is_undefined(exportMinQuality) {
+		exportMinQuality = false
+	}
 
 	isSingleCell := !is_undefined(cellTags) && len(cellTags) > 0
 	hashCellKey := isSingleCell && len(cellTags) > 1
@@ -482,7 +487,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
-				if !isImputed && !isAminoAcid {
+				if !isImputed && !isAminoAcid && exportMinQuality {
 					columnsSpecPerClonotypeNoAggregates += [ {
 							column: "minQual" + featureU,
 							id: "min-qual-" + featureL,

package/src/main.tpl.tengo

@@ -122,7 +122,7 @@ wf.body(func(args) {
 			limitInput: limitInput,
 			perProcessMemGB: perProcessMemGB,
 			perProcessCPUs: perProcessCPUs,
-				highDiversityLibrary: args.highDiversityLibrary,
+				cloneClusteringMode: args.cloneClusteringMode,
 			blockId: blockId,
 			libraryId: libraryId,
 			presetCommonName: args.presetCommonName,
@@ -131,7 +131,8 @@ wf.body(func(args) {
 				rightAlignmentMode: args.rightAlignmentMode,
 				materialType: args.materialType,
 				tagPattern: args.tagPattern,
-				assembleClonesBy: args.assembleClonesBy
+				assembleClonesBy: args.assembleClonesBy,
+				exportMinQuality: args.exportMinQuality
 		})
 	})
 

package/src/mixcr-analyze.tpl.tengo

@@ -143,14 +143,19 @@ self.body(func(inputs) {
 	if !is_undefined(assembleClonesBy) {
 		mixcrCmdBuilder.arg("--assemble-clonotypes-by").arg(assembleClonesBy)
 	}
-	// High diversity library tuning
-	highDiversityLibrary := params.highDiversityLibrary
-	if !is_undefined(highDiversityLibrary) && highDiversityLibrary {
+	// Clone clustering tuning
+	cloneClusteringMode := params.cloneClusteringMode
+	if is_undefined(cloneClusteringMode) {
+		cloneClusteringMode = "default"
+	}
+	if cloneClusteringMode == "relaxed" {
 		mixcrCmdBuilder.
 			arg("-Massemble.cloneAssemblerParameters.minimalQuality=20").
 			arg("-Massemble.cloneAssemblerParameters.badQualityThreshold=10").
 			arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchParameters=oneMismatchOrIndel").
 			arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchDepth=1")
+	} else if cloneClusteringMode == "off" {
+		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters=null")
 	}
 
 	inputMap := inputData.inputs()

package/src/process.tpl.tengo

@@ -203,7 +203,7 @@ self.body(func(inputs) {
 		}
 	} ]
 
-	exportSpecs := calculateExportSpecs(presetSpecForBack, sampleIdAxisSpec, blockId)
+	exportSpecs := calculateExportSpecs(presetSpecForBack, sampleIdAxisSpec, blockId, params.exportMinQuality)
 
 	columnsSpecPerSample := exportSpecs.columnsSpecPerSample
 	columnsSpecPerSampleSc := exportSpecs.columnsSpecPerSampleSc
@@ -273,7 +273,7 @@ self.body(func(inputs) {
 					materialType: params.materialType,
 					tagPattern: params.tagPattern,
 					assembleClonesBy: params.assembleClonesBy,
-					highDiversityLibrary: params.highDiversityLibrary
+					cloneClusteringMode: params.cloneClusteringMode
 				},
 				library: library,
 				presetContent: presetContent

package/src/test/columns-calculate.tpl.tengo

@@ -9,7 +9,7 @@ self.defineOutputs("exportSpecs")
 self.body(func(inputs) {
 	presetSpecForBack := inputs.presetSpecForBack.getDataAsJson()
 
-	exportSpecs := calculateExportSpecs(presetSpecForBack, {}, "test")
+	exportSpecs := calculateExportSpecs(presetSpecForBack, {}, "test", false)
 	exportSpecs = maps.deepMerge(exportSpecs, {
     	axisByClonotypeKeyGen: undefined,
 		axisByScClonotypeKeyGen: undefined,