@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.14.0 → 1.16.0

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@1.14.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.16.0 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
 
+## 1.16.0
+
+### Minor Changes
+
+- 187f583: Fix repseqio fasta generation, dependencies updates
+
+## 1.15.0
+
+### Minor Changes
+
+- a08b796: multiple UMI bug fix
+
 ## 1.14.0
 
 ### Minor Changes

package/dist/tengo/lib/qc-report-columns.lib.tengo

@@ -3,9 +3,13 @@
 
 ll := import("@platforma-sdk/workflow-tengo:ll")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
+text := import("text")
 
 
-getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains) {
+getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains, umiTags) {
+    if is_undefined(umiTags) {
+        umiTags = []
+    }
 
     baseColumns := [
     {
@@ -622,73 +626,82 @@ getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains) {
         bulkOrder -= 100
     }
 
-    dataWithUmiColumns := [    {
-        column: "refineTags.UMI.outputCount",
-        id: "refine-tags-umi-output-count",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputCount",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags UMI - Output Count"
+    dataWithUmiColumns := []
+    for idx, umiTag in umiTags {
+        orderBase := 85000 + idx * 10
+        orderBasePercents := 85100 + idx * 10
+        orderDiversity := 85200 + idx * 10
+        orderDiversityPercents := 85300 + idx * 10
+        tagL := text.to_lower(umiTag)
+        dataWithUmiColumns = dataWithUmiColumns + [{
+            column: "refineTags." + umiTag + ".outputCount",
+            id: "refine-tags-" + tagL + "-output-count",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCount",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(orderBase),
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Count"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputCountPercents",
-        id: "refine-tags-umi-output-count-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputCountPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags UMI - Output Count (%)"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputCountPercents",
+            id: "refine-tags-" + tagL + "-output-count-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCountPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": string(orderBasePercents),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Count (%)"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputDiversity",
-        id: "refine-tags-umi-output-diversity",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputDiversity",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85200",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags UMI - Output Diversity"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputDiversity",
+            id: "refine-tags-" + tagL + "-output-diversity",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversity",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(orderDiversity),
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputDiversityPercents",
-        id: "refine-tags-umi-output-diversity-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputDiversityPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85300",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags UMI - Output Diversity (%)"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputDiversityPercents",
+            id: "refine-tags-" + tagL + "-output-diversity-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversityPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": string(orderDiversityPercents),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity (%)"
+                }
             }
-        }
-    },
-    {
+        }]
+    }
+
+    dataWithUmiColumns = dataWithUmiColumns + [{
         column: "refineTags.numberOfGroupsAccepted",
         id: "refine-tags-number-of-groups-accepted",
         allowNA: true,

package/package.json

@@ -1,17 +1,17 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.14.0",
+  "version": "1.16.0",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.7.3",
+    "@platforma-sdk/workflow-tengo": "^5.8.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-254-develop",
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.4.2",
-    "@platforma-sdk/test": "^1.48.8",
-    "vitest": "^2.1.8"
+    "@platforma-sdk/tengo-builder": "^2.4.11",
+    "@platforma-sdk/test": "^1.52.4",
+    "vitest": "^4.0.17"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/export-report.tpl.tengo

@@ -30,7 +30,8 @@ self.body(func(inputs) {
     isLibraryFileGzipped := inputs.isLibraryFileGzipped
     clonotypeTablesData := inputs.clonotypeTablesData
 
-	hasUmi := !is_undefined(presetSpecForBack.umiTags) && len(presetSpecForBack.umiTags) > 0
+	umiTags := inputs.umiTags
+	hasUmi := !is_undefined(umiTags) && len(umiTags) > 0
 
     chainInfos := {
 	"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
@@ -173,7 +174,7 @@ self.body(func(inputs) {
     
     tsvFile := wfResult.getFile("qc-report-processed.tsv")
 
-    qcReportColumns := qcReportColumns(hasUmi, sampleIdAxisSpec, chains)
+    qcReportColumns := qcReportColumns(hasUmi, sampleIdAxisSpec, chains, umiTags)
     reportColumnsSpec := qcReportColumns.reportColumnsSpec
 
     qcReportTable := xsv.importFile(

package/src/main.tpl.tengo

@@ -32,27 +32,6 @@ wf.body(func(args) {
 	perProcessCPUs := args.perProcessCPUs
 	cloneClusteringMode := args.cloneClusteringMode
 
-	// Create V and J gene FASTA files
-	
-	fastaFileCmdBuilder := exec.builder().cmd("/usr/bin/env").arg("bash")
-	
-	// Save vGene to FASTA file if available
-	if args.vGenes != "" {
-		fastaFileCmdBuilder.writeFile("vGene.fasta", args.vGenes).
-            saveFile("vGene.fasta")
-	}
-	
-	// Save jGene to FASTA file if available
-	if args.jGenes != "" {
-		fastaFileCmdBuilder.writeFile("jGene.fasta", args.jGenes).
-            saveFile("jGene.fasta")
-	}
-
-    fastaFileCmd := fastaFileCmdBuilder.run()
-
-    vGeneFasta := fastaFileCmd.getFile("vGene.fasta")
-    jGeneFasta := fastaFileCmd.getFile("jGene.fasta")
-
 	chainInfos := {
 		"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
 		"IGLight": { mixcrFilter: "IGK", name: "IG Light", shortName: "Light" },
@@ -65,8 +44,8 @@ wf.body(func(args) {
     // Generate reference library using repseqio if both V and J genes are available
   
 	repseqioResults := render.create(repseqioLibraryTpl, {
-		vGeneFasta: vGeneFasta,
-		jGeneFasta: jGeneFasta,
+		vGenes: args.vGenes,
+		jGenes: args.jGenes,
 		chains: chainInfos[chains].mixcrFilter
 	})
 	

package/src/process.tpl.tengo

@@ -34,7 +34,39 @@ self.body(func(inputs) {
 	cloneClusteringMode := params.cloneClusteringMode
 	tagPattern := params.tagPattern
 
-	hasUMI := text.contains(tagPattern, "UMI") || text.contains(tagPattern, "Umi") || text.contains(tagPattern, "umi")
+	extractUmiTags := func(pattern) {
+		if is_undefined(pattern) || pattern == "" {
+			return []
+		}
+		umiTags := []
+		parts := text.split(pattern, "(")
+		for idx, part in parts {
+			if idx == 0 {
+				continue
+			}
+			if !text.contains(part, ":") {
+				continue
+			}
+			name := text.split(part, ":")[0]
+			if !text.has_prefix(text.to_lower(name), "umi") {
+				continue
+			}
+			exists := false
+			for tag in umiTags {
+				if tag == name {
+					exists = true
+					break
+				}
+			}
+			if !exists {
+				umiTags = append(umiTags, name)
+			}
+		}
+		return umiTags
+	}
+
+	umiTags := extractUmiTags(tagPattern)
+	hasUMI := len(umiTags) > 0
 	limitInput := inputs.limitInput
 	perProcessMemGB := params.perProcessMemGB
 	perProcessCPUs := params.perProcessCPUs
@@ -45,7 +77,7 @@ self.body(func(inputs) {
 	presetSpecForBack := {
 		assemblingFeature: params.assemblingFeature,
 		splitByC: true,
-		umiTags: hasUMI ? ["Molecule"] : undefined,
+		umiTags: hasUMI ? umiTags : undefined,
 		cellTags: []
 	}
 
@@ -291,12 +323,13 @@ self.body(func(inputs) {
 
 	qcReportTable := render.create(exportReportTpl, {
 		clnsData: mixcrResults.outputData("clns"),
-		presetSpecForBack: presetSpecForBack,
 		sampleIdAxisSpec: sampleIdAxisSpec,
 		chains: [chains],
 		library: referenceLibrary,
 		isLibraryFileGzipped: false,
-		clonotypeTablesData: clonotypeTablesData
+		clonotypeTablesData: clonotypeTablesData,
+		hasUmi: hasUMI,
+		umiTags: umiTags
 	})
 
 	return {

package/src/qc-report-columns.lib.tengo

@@ -3,9 +3,13 @@
 
 ll := import("@platforma-sdk/workflow-tengo:ll")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
+text := import("text")
 
 // QC Report column specifications function
-getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains) {
+getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains, umiTags) {
+    if is_undefined(umiTags) {
+        umiTags = []
+    }
     // Bulk sequencing columns
     baseColumns := [
     {
@@ -622,73 +626,82 @@ getQcReportColumns := func(hasUmi, sampleIdAxisSpec, chains) {
         bulkOrder -= 100
     }
 
-    dataWithUmiColumns := [    {
-        column: "refineTags.UMI.outputCount",
-        id: "refine-tags-umi-output-count",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputCount",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85000",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags UMI - Output Count"
+    dataWithUmiColumns := []
+    for idx, umiTag in umiTags {
+        orderBase := 85000 + idx * 10
+        orderBasePercents := 85100 + idx * 10
+        orderDiversity := 85200 + idx * 10
+        orderDiversityPercents := 85300 + idx * 10
+        tagL := text.to_lower(umiTag)
+        dataWithUmiColumns = dataWithUmiColumns + [{
+            column: "refineTags." + umiTag + ".outputCount",
+            id: "refine-tags-" + tagL + "-output-count",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCount",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(orderBase),
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Count"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputCountPercents",
-        id: "refine-tags-umi-output-count-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputCountPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85100",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags UMI - Output Count (%)"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputCountPercents",
+            id: "refine-tags-" + tagL + "-output-count-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputCountPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": string(orderBasePercents),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Count (%)"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputDiversity",
-        id: "refine-tags-umi-output-diversity",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputDiversity",
-            valueType: "Long",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/table/orderPriority": "85200",
-                "pl7.app/table/visibility": "optional",
-                "pl7.app/label": "Refine Tags UMI - Output Diversity"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputDiversity",
+            id: "refine-tags-" + tagL + "-output-diversity",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversity",
+                valueType: "Long",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/table/orderPriority": string(orderDiversity),
+                    "pl7.app/table/visibility": "optional",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity"
+                }
             }
-        }
-    },
-    {
-        column: "refineTags.UMI.outputDiversityPercents",
-        id: "refine-tags-umi-output-diversity-percents",
-        allowNA: true,
-        naRegex: "NaN",
-        spec: {
-            name: "mixcr.com/reports/refineTags/UMI/outputDiversityPercents",
-            valueType: "Double",
-            annotations: {
-                "pl7.app/min": "0",
-                "pl7.app/max": "100",
-                "pl7.app/table/orderPriority": "85300",
-                "pl7.app/table/visibility": "default",
-                "pl7.app/label": "Refine Tags UMI - Output Diversity (%)"
+        },
+        {
+            column: "refineTags." + umiTag + ".outputDiversityPercents",
+            id: "refine-tags-" + tagL + "-output-diversity-percents",
+            allowNA: true,
+            naRegex: "NaN",
+            spec: {
+                name: "mixcr.com/reports/refineTags/" + umiTag + "/outputDiversityPercents",
+                valueType: "Double",
+                annotations: {
+                    "pl7.app/min": "0",
+                    "pl7.app/max": "100",
+                    "pl7.app/table/orderPriority": string(orderDiversityPercents),
+                    "pl7.app/table/visibility": "default",
+                    "pl7.app/label": "Refine Tags " + umiTag + " - Output Diversity (%)"
+                }
             }
-        }
-    },
-    {
+        }]
+    }
+
+    dataWithUmiColumns = dataWithUmiColumns + [{
         column: "refineTags.numberOfGroupsAccepted",
         id: "refine-tags-number-of-groups-accepted",
         allowNA: true,

package/src/repseqio-library.tpl.tengo

@@ -12,9 +12,6 @@ repseqioSw := assets.importSoftware("@platforma-open/milaboratories.software-rep
 self.defineOutputs("referenceLibrary", "debugOutput")
 
 self.body(func(inputs) {
-	// Get V and J gene FASTA files from prerun
-	vGeneFasta := inputs.vGeneFasta
-	jGeneFasta := inputs.jGeneFasta
 	
 	// Create repseqio command to generate reference library
 	repseqioVgeneCmd := exec.builder().
@@ -26,7 +23,8 @@ self.body(func(inputs) {
 		arg("--taxon-id").arg("1111").
 		arg("--gene-feature").arg("VRegion").
 		arg("--name-index").arg("0").
-		arg("vGene.fasta").addFile("vGene.fasta", vGeneFasta).
+		writeFile("vGene.fasta", inputs.vGenes).saveFile("vGene.fasta").
+		arg("vGene.fasta").
 		arg("vGene.json").saveFile("vGene.json").
 		cpu(1).mem("4GB")
 	
@@ -35,6 +33,7 @@ self.body(func(inputs) {
 	
 	// Get the generated reference library file
 	referenceLibraryVgene := repseqioVgeneResult.getFile("vGene.json")
+	vGeneFasta := repseqioVgeneResult.getFile("vGene.fasta")
 
 	repseqioJgeneCmd := exec.builder().
 		software(repseqioSw).
@@ -45,13 +44,14 @@ self.body(func(inputs) {
 		arg("--taxon-id").arg("1111").
 		arg("--gene-feature").arg("JRegion").
 		arg("--name-index").arg("0").
-		arg("jGene.fasta").addFile("jGene.fasta", jGeneFasta).
+		writeFile("jGene.fasta", inputs.jGenes).saveFile("jGene.fasta").
+		arg("jGene.fasta").
 		arg("jGene.json").saveFile("jGene.json").
 		cpu(1).mem("4GB")
 	
 	repseqioJgeneResult := repseqioJgeneCmd.run()
 	referenceLibraryJgene := repseqioJgeneResult.getFile("jGene.json")
-
+	jGeneFasta := repseqioJgeneResult.getFile("jGene.fasta")
 	repseqioMergeCmd := exec.builder().
 		software(repseqioSw).
 		arg("merge").