@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.16.0 → 3.17.1

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@3.16.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.17.1 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
 
+## 3.17.1
+
+### Patch Changes
+
+- 5d90233: Hide non-relevant columns
+
+## 3.17.0
+
+### Minor Changes
+
+- 480dfc5: generic presets added
+
 ## 3.16.0
 
 ### Minor Changes

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

@@ -73,6 +73,9 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		} else if len(splittedFeature2) == 2 {
 			if splittedFeature2[0] == "{CDR3Begin" {
 				productiveFeature = assemblingFeature
+			} else if splittedFeature2[0] == "{FR3Begin" {
+				productiveFeature = assemblingFeature
+				coreVFeature = "FR3"
 			} else {
 				productiveFeature = assemblingFeature
 				coreVFeature = splittedFeature2[0]+":FR3End}"
@@ -257,13 +260,14 @@ 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"
 			})
 		}
@@ -338,13 +342,14 @@ 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"
 				})
 			}

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.16.0",
+  "version": "3.17.1",
   "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

@@ -73,6 +73,9 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		} else if len(splittedFeature2) == 2 {
 			if splittedFeature2[0] == "{CDR3Begin" {
 				productiveFeature = assemblingFeature
+			} else if splittedFeature2[0] == "{FR3Begin" {
+				productiveFeature = assemblingFeature
+				coreVFeature = "FR3"
 			} else {
 				productiveFeature = assemblingFeature
 				coreVFeature = splittedFeature2[0]+":FR3End}"
@@ -257,13 +260,14 @@ 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"
 			})
 		}
@@ -338,13 +342,14 @@ 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"
 				})
 			}

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

@@ -11,7 +11,12 @@ self.validateInputs({
 	preset: "any",
 	params: {
 		"__options__,closed": "",
-		"species,omitempty": "string"
+		"species,omitempty": "string",
+		"leftAlignmentMode,omitempty": "string",
+		"rightAlignmentMode,omitempty": "string",
+		"materialType,omitempty": "string",
+		"tagPattern,omitempty": "string",
+		"assembleClonesBy,omitempty": "string"
 	}
 })
 
@@ -22,6 +27,11 @@ self.defineOutputs("preset", "presetSpecForBack")
 self.body(func(inputs) {
 	preset := inputs.preset
 	species := inputs.params.species
+	leftAlignmentMode := inputs.params.leftAlignmentMode
+	rightAlignmentMode := inputs.params.rightAlignmentMode
+	materialType := inputs.params.materialType
+	tagPattern := inputs.params.tagPattern
+	assembleClonesBy := inputs.params.assembleClonesBy
 
 	mixcrExportPresetCmdBuilder := exec.builder().
 		inLightQueue().
@@ -47,6 +57,22 @@ self.body(func(inputs) {
 		mixcrExportPresetCmdBuilder.arg("--species").arg(species)
 	}
 
+	if !is_undefined(leftAlignmentMode) {
+		mixcrExportPresetCmdBuilder.arg(leftAlignmentMode)
+	}
+	if !is_undefined(rightAlignmentMode) {
+		mixcrExportPresetCmdBuilder.arg(rightAlignmentMode)
+	}
+	if !is_undefined(materialType) {
+		mixcrExportPresetCmdBuilder.arg(materialType)
+	}
+	if !is_undefined(tagPattern) {
+		mixcrExportPresetCmdBuilder.arg("--tag-pattern").arg(tagPattern)
+	}
+	if !is_undefined(assembleClonesBy) {
+		mixcrExportPresetCmdBuilder.arg("--assemble-clonotypes-by").arg(assembleClonesBy)
+	}
+
 	mixcrExportPresetCmd := mixcrExportPresetCmdBuilder.arg("preset.json").
 		saveFileContent("preset.json").
 		saveFile("preset.json").

package/src/main.tpl.tengo

@@ -86,7 +86,12 @@ wf.body(func(args) {
 	presetInfoResult := render.create(calculatePresetInfoTpl, {
 		preset: presetResource,
 		params: {
-			species: species
+			species: species,
+			leftAlignmentMode: args.leftAlignmentMode,
+			rightAlignmentMode: args.rightAlignmentMode,
+			materialType: args.materialType,
+			tagPattern: args.tagPattern,
+			assembleClonesBy: args.assembleClonesBy
 		}
 	})
 
@@ -111,7 +116,7 @@ wf.body(func(args) {
 
 		library: library,
 
-		params: smart.createJsonResource({
+			params: smart.createJsonResource({
 			species: species,
 			receptorsOrChains: receptorsOrChains,
 			limitInput: limitInput,
@@ -121,7 +126,12 @@ wf.body(func(args) {
 			blockId: blockId,
 			libraryId: libraryId,
 			presetCommonName: args.presetCommonName,
-			isLibraryFileGzipped: isLibraryFileGzipped
+				isLibraryFileGzipped: isLibraryFileGzipped,
+				leftAlignmentMode: args.leftAlignmentMode,
+				rightAlignmentMode: args.rightAlignmentMode,
+				materialType: args.materialType,
+				tagPattern: args.tagPattern,
+				assembleClonesBy: args.assembleClonesBy
 		})
 	})
 

package/src/mixcr-analyze.tpl.tengo

@@ -29,6 +29,11 @@ self.body(func(inputs) {
 	params := inputs.params
 	species := params.species
 	limitInput := params.limitInput
+	leftAlignmentMode := params.leftAlignmentMode
+	rightAlignmentMode := params.rightAlignmentMode
+	materialType := params.materialType
+	tagPattern := params.tagPattern
+	assembleClonesBy := params.assembleClonesBy
 	perProcessMemGB := inputs.perProcessMemGB
 	perProcessCPUs := inputs.perProcessCPUs
 	fileExtension := params.fileExtension
@@ -122,6 +127,22 @@ self.body(func(inputs) {
 			arg(preset.name)
 	}
 
+	// Optional preset-specific parameters (order matters if preset requires positional values)
+	if !is_undefined(leftAlignmentMode) {
+		mixcrCmdBuilder.arg(leftAlignmentMode)
+	}
+	if !is_undefined(rightAlignmentMode) {
+		mixcrCmdBuilder.arg(rightAlignmentMode)
+	}
+	if !is_undefined(materialType) {
+		mixcrCmdBuilder.arg(materialType)
+	}
+	if !is_undefined(tagPattern) {
+		mixcrCmdBuilder.arg("--tag-pattern").arg(tagPattern)
+	}
+	if !is_undefined(assembleClonesBy) {
+		mixcrCmdBuilder.arg("--assemble-clonotypes-by").arg(assembleClonesBy)
+	}
 	// High diversity library tuning
 	highDiversityLibrary := params.highDiversityLibrary
 	if !is_undefined(highDiversityLibrary) && highDiversityLibrary {

package/src/prerun.tpl.tengo

@@ -49,10 +49,16 @@ wf.body(func(args) {
 			ll.assert(preset.type == "name", "unexpected preset type")
 			// whole json, including type
 			presetResource = smart.createJsonResource(preset)
+			isGenericPreset := args.isGenericPreset
 			presetInfoResult := render.create(calculatePresetInfoTpl, {
 				preset: presetResource,
 				params: {
-					species: args.species
+					species: args.species,
+					leftAlignmentMode: args.leftAlignmentMode,
+					rightAlignmentMode: args.rightAlignmentMode,
+					materialType: args.materialType,
+					tagPattern: isGenericPreset ? "^(R1:*)\\^(R2:*)" : undefined,
+					assembleClonesBy: isGenericPreset ? "CDR3" : undefined
 				}
 			})
 			outputs.preset = presetInfoResult.output("presetSpecForBack", 24 * 60 * 60 * 1000)

package/src/process.tpl.tengo

@@ -268,6 +268,11 @@ self.body(func(inputs) {
 					fileExtension: fileExtension,
 					reports: reports,
 					isLibraryFileGzipped: isLibraryFileGzipped,
+					leftAlignmentMode: params.leftAlignmentMode,
+					rightAlignmentMode: params.rightAlignmentMode,
+					materialType: params.materialType,
+					tagPattern: params.tagPattern,
+					assembleClonesBy: params.assembleClonesBy,
 					highDiversityLibrary: params.highDiversityLibrary
 				},
 				library: library,
@@ -452,12 +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
 				},
@@ -583,9 +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)
@@ -625,7 +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,