@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.17.0 → 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@3.17.0 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 +1,17 @@
 # @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
+
+- 5d90233: Hide non-relevant columns
+
 ## 3.17.0
 
 ### Minor 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
@@ -260,13 +265,14 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 		spec: {
 			name: "pl7.app/vdj/readFractionMean",
 			valueType: "Double",
-			annotations: a(87130, true, {
+			annotations: a(87130, false, {
 				"pl7.app/min": "0",
 				"pl7.app/max": "1",
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
 				"pl7.app/label": "Mean Fraction of Reads",
+				"pl7.app/description": "The average read fraction of a clonotype across all samples where it is present.",
 				"pl7.app/format": ".2p"
 			})
 		}
@@ -341,13 +347,14 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueMoleculeFractionMean",
 				valueType: "Double",
-				annotations: a(87130, true, {
+				annotations: a(87130, false, {
 					"pl7.app/min": "0",
 					"pl7.app/max": "1",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "molecules",
 					"pl7.app/abundance/normalized": "true",
 					"pl7.app/label": "Mean Fraction of UMIs",
+					"pl7.app/description": "The average UMI fraction of a clonotype across all samples where it is present.",
 					"pl7.app/format": ".2p"
 				})
 			}
@@ -480,7 +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

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.17.0",
+  "version": "3.18.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.6.5",
+    "@platforma-sdk/workflow-tengo": "^5.6.6",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-254-develop"
   },
   "devDependencies": {
-    "@milaboratories/ts-configs": "^1.0.6",
-    "@platforma-sdk/tengo-builder": "^2.3.14",
-    "@platforma-sdk/test": "^1.46.5",
+    "@milaboratories/ts-configs": "^1.1.0",
+    "@platforma-sdk/tengo-builder": "^2.4.1",
+    "@platforma-sdk/test": "^1.47.6",
     "vitest": "~4.0.15",
     "typescript": "~5.6.3"
   },

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
@@ -260,13 +265,14 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 		spec: {
 			name: "pl7.app/vdj/readFractionMean",
 			valueType: "Double",
-			annotations: a(87130, true, {
+			annotations: a(87130, false, {
 				"pl7.app/min": "0",
 				"pl7.app/max": "1",
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
 				"pl7.app/label": "Mean Fraction of Reads",
+				"pl7.app/description": "The average read fraction of a clonotype across all samples where it is present.",
 				"pl7.app/format": ".2p"
 			})
 		}
@@ -341,13 +347,14 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueMoleculeFractionMean",
 				valueType: "Double",
-				annotations: a(87130, true, {
+				annotations: a(87130, false, {
 					"pl7.app/min": "0",
 					"pl7.app/max": "1",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "molecules",
 					"pl7.app/abundance/normalized": "true",
 					"pl7.app/label": "Mean Fraction of UMIs",
+					"pl7.app/description": "The average UMI fraction of a clonotype across all samples where it is present.",
 					"pl7.app/format": ".2p"
 				})
 			}
@@ -480,7 +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
@@ -457,12 +457,35 @@ self.body(func(inputs) {
 		} ]
 
 		if !isSingleCell {
+			// Modify column visibility for TCR chains
+			isTCRChain := text.has_prefix(chain, "TCR")
+			columnsForAggregation := columnsSpecPerClonotypeNoAggregates + columnsSpecPerClonotypeAggregates
+			if isTCRChain {
+				visibilitySettings := {
+					"bestCGene":      "optional",
+					"bestCHit":       "optional",
+					"isotypePrimary": "hidden"
+				}
+				columnsForAggregation = slices.map(columnsForAggregation, func(col) {
+					visibility := visibilitySettings[col.column]
+					if !is_undefined(visibility) {
+						return maps.deepMerge(col, {
+							spec: {
+								annotations: maps.merge(col.spec.annotations, {
+									"pl7.app/table/visibility": visibility
+								})
+							}
+						})
+					}
+					return col
+				})
+			}
 			aggregationOutputs += [ {
 				type: "Xsv",
 				xsvType: "tsv",
 				settings: {
 					axes: [ axisByClonotypeKeyGen(chain) ],
-					columns: columnsSpecPerClonotypeNoAggregates + columnsSpecPerClonotypeAggregates,
+					columns: columnsForAggregation,
 					storageFormat: "Parquet",
 					partitionKeyLength: 0
 				},
@@ -588,9 +611,34 @@ self.body(func(inputs) {
 			for chainIdx in [0, 1] {
 				// "A" chain is always the one that is more diverse
 				chainLetterU := ["A", "B"][chainIdx]
-				chainNameU := chainInfos[receptorInfo.chains[chainIdx]].shortName
+				chain := receptorInfo.chains[chainIdx]
+				chainNameU := chainInfos[chain].shortName
 				chainNameL := text.to_lower(chainNameU)
 
+				// Modify column visibility for TCR chains
+				isTCRChain := text.has_prefix(chain, "TCR")
+				columnsForSingleCell := columnsSpecPerClonotypeNoAggregates
+				if isTCRChain {
+					visibilitySettings := {
+						"bestCGene":      "optional",
+						"bestCHit":       "optional",
+						"isotypePrimary": "hidden"
+					}
+					columnsForSingleCell = slices.map(columnsForSingleCell, func(col) {
+					visibility := visibilitySettings[col.column]
+					if !is_undefined(visibility) {
+						return maps.deepMerge(col, {
+							spec: {
+								annotations: maps.merge(col.spec.annotations, {
+									"pl7.app/table/visibility": visibility
+								})
+							}
+						})
+					}
+					return col
+					})
+				}
+
 				for isPrimary in [true, false] {
 					pPrefixU := isPrimary ? "Primary" : "Secondary"
 					pPrefixL := text.to_lower(pPrefixU)
@@ -630,7 +678,7 @@ self.body(func(inputs) {
 						xsvType: "tsv",
 						settings: {
 							axes: [ axisByScClonotypeKeyGen(receptor) ],
-							columns: transformSpecs(isPrimary ? columnsSpecPerClonotypeNoAggregates : columnsSpecPerClonotypeSecondary, {
+							columns: transformSpecs(isPrimary ? columnsForSingleCell : columnsSpecPerClonotypeSecondary, {
 								spec: {
 									domain: {
 										"pl7.app/vdj/scClonotypeChain": chainLetterU,

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,