@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.1.1 → 3.2.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.1.1",
+  "version": "3.2.1",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^5.0.3",

package/src/aggregate-by-clonotype-key.tpl.tengo

@@ -41,7 +41,7 @@ self.body(func(inputs) {
 
 	baseSchemaForRead := schemaPerSample + [ { column: "clonotypeKey", type: "String" } ]
 
-	ll.print("__THE_LOG__ AGGREGATE BY CLONOTYPE KEY: " + json.encode(maps.getKeys(inputMap)))
+	// ll.print("__THE_LOG__ AGGREGATE BY CLONOTYPE KEY: " + json.encode(maps.getKeys(inputMap)))
 
 	for sKey in maps.getKeys(inputMap) {
 		inputFile := inputMap[sKey]

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

@@ -545,12 +545,11 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	junctionTypes := [ "VJ", "VD", "DJ" ]
 	for junctionType in junctionTypes {
 		feature := junctionType + "Junction"
-		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
 
 		columnsSpecPerClonotypeNoAggregates += [ {
 			column: "nLength" + feature,
 			id: "n-length-" + text.to_lower(junctionType) + "-junction",
-			naRegex: naRegex,
+			naRegex: "^[a-z_]*$",
 			allowNA: true,
 			spec: {
 				name: "pl7.app/vdj/sequenceLength",
@@ -572,7 +571,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 	columnsSpecPerClonotypeNoAggregates += [ {
 		column: "nLengthTotalAdded",
 		id: "n-length-total-added",
-		naRegex: "region_not_covered|no_d_gene",
+		naRegex: "^[a-z_]*$",
 		allowNA: true,
 		spec: {
 			name: "pl7.app/vdj/sequenceLength",

package/src/export-report.tpl.tengo

@@ -24,11 +24,14 @@ ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptab
 
 self.body(func(inputs) {
     clnsData := inputs.clnsData
-    isSingleCell := inputs.isSingleCell
-    hasUmi := inputs.hasUmi
+    presetSpecForBack := inputs.presetSpecForBack
     sampleIdAxisSpec := inputs.sampleIdAxisSpec
     chains := inputs.chains
 
+    isSingleCell := len(presetSpecForBack.cellTags) > 0
+	hasUmi := !is_undefined(presetSpecForBack.umiTags) && len(presetSpecForBack.umiTags) > 0
+    cellTags := presetSpecForBack.cellTags
+
     chainInfos := {
 	"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
 	"IGLight": { mixcrFilter: "IGK,IGL", name: "IG Light", shortName: "Light" },
@@ -98,7 +101,7 @@ self.body(func(inputs) {
     
     tsvFile := wfResult.getFile("qc-report-processed.tsv")
 
-    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chainsForMixcr)
+    qcReportColumns := qcReportColumns(hasUmi, isSingleCell, sampleIdAxisSpec, chainsForMixcr, cellTags)
     reportColumnsSpec := qcReportColumns.reportColumnsSpec
 
     qcReportTable := xsv.importFile(

package/src/mixcr-export.tpl.tengo

@@ -35,6 +35,7 @@ self.body(func(inputs) {
 	}
 
 	mainAbundanceColumnUnnormalizedArgs := params.mainAbundanceColumnUnnormalizedArgs
+	mainAbundanceColumnIsReadCount := params.mainAbundanceColumnIsReadCount == true
 	mainIsProductiveArgs := params.mainIsProductiveArgs
 
 	hashKeyDerivationExpressionPt := func(sourceColumns) {
@@ -145,7 +146,22 @@ self.body(func(inputs) {
 			mem("4GiB").
 			cpu(2)
 
-		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, { xsvType: "tsv", inferSchema: false })
+		frameLoadOps := {
+			xsvType: "tsv",
+			inferSchema: false
+		}
+
+		if mainAbundanceColumnIsReadCount {
+			frameLoadOps.schema = [ { column: "readCount", type: "Double" } ]
+		}
+
+		dfSingleCell := wfSingleCell.frame(unprocessedTsvForSingleCell, frameLoadOps)
+
+		if mainAbundanceColumnIsReadCount {
+			dfSingleCell.addColumns(
+				pt.col("readCount").round().cast("Long").alias("readCount")
+			)
+		}
 
 		dfSingleCell.addColumns(
 			hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey"),

package/src/process-single-cell.tpl.tengo

@@ -22,7 +22,7 @@ self.defineOutputs("abundanceTsv", "clonotypeTsv",
 ptablerSw := assets.importSoftware("@platforma-open/milaboratories.software-ptabler:main")
 
 self.body(func(inputs) {
-	ll.print("__THE_LOG__ PROCESS SINGLE CELL")
+	// ll.print("__THE_LOG__ PROCESS SINGLE CELL")
 
 	byCellTagA := inputs[pConstants.VALUE_FIELD_NAME]
 	inputDataMeta := byCellTagA.getDataAsJson()

package/src/process.tpl.tengo

@@ -391,7 +391,7 @@ self.body(func(inputs) {
 				stepCache: 30 * times.minute,
 
 				extra: {
-					params: {
+					params: maps.clone({
 						chains: chainInfo.mixcrFilter,
 						clonotypeKeyColumns: clonotypeKeyColumns,
 						clonotypeKeyArgs: clonotypeKeyArgs,
@@ -406,9 +406,11 @@ self.body(func(inputs) {
 						cellTagColumns: cellTagColumns,
 						hashCellKey: hashCellKey,
 
+						mainAbundanceColumnIsReadCount: (!is_undefined(cellTagColumns) && len(cellTagColumns) > 0 && mainAbundanceColumnUnnormalized == "readCount") ? true : undefined,
+
 						exportArgs: exportArgs,
 						isLibraryFileGzipped: isLibraryFileGzipped
-					},
+					}, { removeUndefs: true }),
 					library: library
 				}
 			}
@@ -675,14 +677,21 @@ self.body(func(inputs) {
 			singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBPrimary", "clonotypeProperties/" + receptor + "/bPrimary/")
 			singleCellResult.addXsvOutputToBuilder(clonotypes, "propertiesBSecondary", "clonotypeProperties/" + receptor + "/bSecondary/")
 
-			singleCellResult.addXsvOutputToBuilder(clonotypes, "cellsLinkerTable", "clonotypeProperties/" + receptor + "/cellsLinkerTable/")
+			for columnName in singleCellResult.listXsvColumns("cellsLinkerTable") {
+				anonymizedData := singleCellResult.outputData("cellsLinkerTable", columnName)
+				clonotypes.add(
+					"clonotypeProperties/" + receptor + "/cellsLinkerTable/" + columnName,
+					singleCellResult.outputSpec("cellsLinkerTable", columnName),
+					anonymize.deanonymizePKeys(anonymizedData, 0, [0], anonymizationResult.mapping)
+				)
+				resultsToCache["clonotypeProperties/" + receptor + "/cellsLinkerTable/" + columnName] = anonymizedData
+			}
 		}
 	}
 
 	qcReportTable := render.create(exportReportTpl, {
 		clnsData: mixcrResults.outputData("clns"),
-		isSingleCell: isSingleCell,
-		hasUmi: hasUmi,
+		presetSpecForBack: presetSpecForBack,
 		sampleIdAxisSpec: sampleIdAxisSpec,
 		chains: chains
 	})