@platforma-open/milaboratories.immune-assay-data.workflow 1.6.1 → 1.6.3

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/immune-assay-data/immune-assay-data/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.immune-assay-data.workflow@1.6.1 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
+> @platforma-open/milaboratories.immune-assay-data.workflow@1.6.3 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/build-outputs.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # @platforma-open/milaboratories.immune-assay-data.workflow
 
+## 1.6.3
+
+### Patch Changes
+
+- 7b51d0b: Fix performance issue
+
+## 1.6.2
+
+### Patch Changes
+
+- c903a35: Add MSA
+- b85d0b1: Update SDK again
+- f5ad6b1: Add MSA
+
 ## 1.6.1
 
 ### Patch Changes

package/package.json

@@ -1,18 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.immune-assay-data.workflow",
-  "version": "1.6.1",
+  "version": "1.6.3",
   "type": "module",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.8.0",
+    "@platforma-sdk/workflow-tengo": "5.9.0",
     "@platforma-open/soedinglab.software-mmseqs2": "^1.17.2",
-    "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.prepare-fasta": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.add-header": "1.1.3",
-    "@platforma-open/milaboratories.immune-assay-data.fasta-to-tsv": "1.1.3"
+    "@platforma-open/milaboratories.immune-assay-data.fasta-to-tsv": "1.1.3",
+    "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.1.3"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.8"
+    "@platforma-sdk/tengo-builder": "2.4.25"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/build-outputs.tpl.tengo

@@ -201,6 +201,47 @@ self.body(func(inputs) {
 		{ splitDataAndSpec: true, cpu: 1, mem: "16GiB" }
 	)
 
+	// Create Linker pFrame connecting Clonotype ID to Assay Sequence Id
+	assayLinkerPframe := xsv.importFile(
+		inputs.bestAlignmentTsv, "tsv", {
+			axes: [
+				{
+					column: "query",
+					spec: inputs.datasetSpec.axesSpec[1]
+				},
+				{
+					column: "target",
+					spec: {
+						name: "pl7.app/vdj/assay/sequenceId",
+						type: "String",
+						domain: {
+							"pl7.app/blockId": inputs.blockId
+						},
+						annotations: {
+							"pl7.app/label": "Sequence Id",
+							"pl7.app/table/fontFamily": "monospace"
+						}
+					}
+				}
+			],
+			columns: [{
+				column: "link",
+				spec: {
+					name: "pl7.app/vdj/link",
+					valueType: "Int",
+					annotations: {
+						"pl7.app/isLinkerColumn": "true",
+						"pl7.app/label": "Clone to assay link",
+						"pl7.app/table/visibility": "hidden"
+					}
+				}
+			}],
+			storageFormat: "Parquet",
+			partitionKeyLength: 0
+		},
+		{ cpu: 1, mem: "16GiB" }
+	)
+
 	// Create informative label with relevant matching parameters
 	identityStr := string(inputs.settings.identity)
 	coverageStr := string(inputs.settings.coverageThreshold)
@@ -226,7 +267,8 @@ self.body(func(inputs) {
 
 	return {
 		assayPframe: assayPframe,
-		epf: epf
+		epf: epf,
+		assayLinkerPframe: pframes.exportFrame(assayLinkerPframe)
 	}
 })
 

package/src/main.tpl.tengo

@@ -265,11 +265,13 @@ wf.body(func(args) {
 
 	assayPframe := undefined
 	epf := undefined
+	assayLinkerPframe := undefined
 	uniqueValuesMap := undefined
 
 	if emptyResults {
 		assayPframe = pframes.emptyPFrame()
 		epf = pframes.emptyPFrame()
+		assayLinkerPframe = pframes.emptyPFrame()
 	} else {
 		//////// Process tables ////////
 		ptw := pt.workflow()
@@ -295,6 +297,12 @@ wf.body(func(args) {
 		}
 		
 		df = df.groupBy("query").agg(cols...)
+		
+		// Add link column for linker pFrame (assayLinkerPframe)
+		df = df.withColumns(
+			pt.lit(1).cast("Int64").alias("link")
+		)
+		
 		df.save("results.tsv")
 
 		// assay data import summary
@@ -374,6 +382,7 @@ wf.body(func(args) {
 			assaySequenceType: assaySequenceType,
 			blockId: blockId,
 			datasetSpec: datasetSpec,
+			bestAlignmentTsv: ptw.getFile("results.tsv"),
 			assayDataTsv: ptw.getFile("assayData.tsv"),
 			clonesDataTsv: ptw.getFile("clonesData.tsv"),
 			uniqueValuesMap: uniqueValuesMap,
@@ -383,12 +392,14 @@ wf.body(func(args) {
 		})
 		assayPframe = buildOutputsResult.output("assayPframe")
 		epf = buildOutputsResult.output("epf")
+		assayLinkerPframe = buildOutputsResult.output("assayLinkerPframe")
 	}
 
 	result := {
 		outputs: {
 			dataImportHandle: importFile.handle,
 			table: assayPframe,
+			assayLinkerPframe: assayLinkerPframe,
 			mmseqsOutput: mmseqsOutput, // @TODO tmp fix to resolve CID conflicts
 			emptyResults: emptyResults		}
 	}