@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.10.3 → 1.12.0

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@1.10.3 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.12.0 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 +1,21 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.12.0
+
+### Minor Changes
+
+- 75ca0ce: change isProductive column values to true and false, sdk update
+
+## 1.11.0
+
+### Minor Changes
+
+- 4f1e226: export of raw mixcr data added
+
+### Patch Changes
+
+- 3d3e04d: updating dependencies
+
 ## 1.10.3
 
 ### Patch Changes

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

@@ -508,7 +508,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 					annotations: a(orderP, variant.visibility, {
 						"pl7.app/label": variant.label,
 						"pl7.app/isDiscreteFilter": "true",
-						"pl7.app/discreteValues": string(json.encode(["True", "False"])) } )
+						"pl7.app/discreteValues": string(json.encode(["true", "false"])) } )
 				}
 			}
 		] 

package/package.json

@@ -1,16 +1,16 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.10.3",
+  "version": "1.12.0",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.4.2",
+    "@platforma-sdk/workflow-tengo": "^5.5.9",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-235-develop",
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.3.2",
-    "@platforma-sdk/test": "^1.44.19",
+    "@platforma-sdk/tengo-builder": "^2.3.3",
+    "@platforma-sdk/test": "^1.45.11",
     "vitest": "^2.1.8"
   },
   "scripts": {

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

@@ -508,7 +508,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 					annotations: a(orderP, variant.visibility, {
 						"pl7.app/label": variant.label,
 						"pl7.app/isDiscreteFilter": "true",
-						"pl7.app/discreteValues": string(json.encode(["True", "False"])) } )
+						"pl7.app/discreteValues": string(json.encode(["true", "false"])) } )
 				}
 			}
 		] 

package/src/main.tpl.tengo

@@ -114,6 +114,7 @@ wf.body(func(args) {
 		clones: pframes.exportFrame(runMixcr.output("clones")),
 		clns: runMixcr.output("clns.data"),
 		progress: runMixcr.output("progress.data"),
+		clonotypeTables: pframes.exportFrame(runMixcr.output("clonotypeTables")),
 		debugOutput: debugOutput
 	}
 

package/src/mixcr-export.tpl.tengo

@@ -6,6 +6,7 @@ slices := import("@platforma-sdk/workflow-tengo:slices")
 assets := import("@platforma-sdk/workflow-tengo:assets")
 exec := import("@platforma-sdk/workflow-tengo:exec")
 pt := import("@platforma-sdk/workflow-tengo:pt")
+clonotypeLabel := import(":clonotype-label")
 
 json := import("json")
 
@@ -20,6 +21,7 @@ self.body(func(inputs) {
 	exportArgs := params.exportArgs
 
 	clonotypeKeyColumns := params.clonotypeKeyColumns
+	mainIsProductiveColumn := params.mainIsProductiveColumn
 
 	hashKeyDerivationExpressionPt := func(sourceColumns) {
 		return pt.concatStr(
@@ -86,10 +88,22 @@ self.body(func(inputs) {
 	dfMain.addColumns(
 		pt.col("readCount").round().cast("Long").alias("readCount")
 	)
+	// Normalize isProductive column casing to strictly "true"/"false"
+	if !is_undefined(mainIsProductiveColumn) {
+		dfMain.addColumns(
+			pt.when(pt.col(mainIsProductiveColumn).strToUpper().eq("TRUE")).
+				then(pt.lit("true")).
+				otherwise(pt.lit("false")).
+				alias(mainIsProductiveColumn)
+		)
+	}
 	dfMain.addColumns(
 		hashKeyDerivationExpressionPt(clonotypeKeyColumns).alias("clonotypeKey")
 	)
 
+	// Generate clonotypeLabel (C-XXXXX or C-XXXXX-RANK) from clonotypeKey
+	dfMain = clonotypeLabel.addClonotypeLabelColumnsPt(dfMain, "clonotypeKey", "clonotypeLabel", pt)
+
 	dfMain.save("output.tsv")
 	ptablerResultMain := wfMain.run()
 	processedTsv := ptablerResultMain.getFile("output.tsv")

package/src/process.tpl.tengo

@@ -183,6 +183,8 @@ self.body(func(inputs) {
 			spec: { domain: { "pl7.app/vdj/chain": chains } }
 		}) ]
 
+	clonotypeTables := pframes.pFrameBuilder()
+
 	exportOutputs := [ {
 		type: "Resource",
 		spec: {
@@ -220,12 +222,15 @@ self.body(func(inputs) {
 					clonotypeKeyColumns: clonotypeKeyColumns,
 					exportArgs: exportArgs,
 					referenceLibrary: referenceLibrary,
-					mixcrChains: mixcrChains
+						mixcrChains: mixcrChains,
+						mainIsProductiveColumn: mainIsProductiveColumn
 				}
 			}
 		}
 	)
 
+	clonotypeTables.add(mixcrChains, exportResults.outputSpec("clonotypeTable"), exportResults.outputData("clonotypeTable"))
+
 	// Aggregate by clonotype key
 	aggregationOutputs := [ {
 		type: "Resource",
@@ -293,6 +298,7 @@ self.body(func(inputs) {
 
 		"progress.data": mixcrResults.outputData("log"),
 
-		clones: clones.build()
+		clones: clones.build(),
+		clonotypeTables: clonotypeTables.build()
 	}
 })