@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.9.0 → 1.10.1

package/.turbo/turbo-build.log

@@ -1,9 +1,8 @@
  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@1.9.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.10.1 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
-  info: Skipping unknown file type: wf.test.ts
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
 Processing "src/calculate-export-specs.lib.tengo"...
 Processing "src/clonotype-label.lib.tengo"...
@@ -13,7 +12,6 @@ Processing "src/mixcr-export.tpl.tengo"...
 Processing "src/process.tpl.tengo"...
 Processing "src/repseqio-library.tpl.tengo"...
 No syntax errors found.
-  info: Skipping unknown file type: wf.test.ts
   info: Compiling 'dist'...
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/lib/clonotype-label.lib.tengo

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.10.1
+
+### Patch Changes
+
+- 2209c82: [sdk/ui] Broken error propagation: block errors are not showing anymore
+
+## 1.10.0
+
+### Minor Changes
+
+- 07e7fc7: Update frame shift behaviour, general refactoring
+
 ## 1.9.0
 
 ### Minor Changes

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

@@ -11,15 +11,6 @@ a := func(order, defaultVisibility, spec) {
 	})
 }
 
-
-
-
-
-inFrameFeatures := {
-	"FR4": "FR4InFrame",
-	"VDJRegion": "VDJRegionInFrame"
-}
-
 annotationMappings := {
 	"CDRs": "{\"1\":\"CDR1\",\"2\":\"CDR2\",\"3\":\"CDR3\"}",
 	"Segments": "{\"1\":\"V\",\"2\":\"D\",\"3\":\"J\",\"4\":\"C\"}"
@@ -47,7 +38,7 @@ toCombinedDomainValue := func(spec) {
 
 
 assemblingFeature := "VDJRegion"
-productiveFeature := "VDJRegionInFrame"
+productiveFeature := "VDJRegion"
 coreVFeature := "{FR1Begin:FR3End}"
 coreJFeature := "FR4"
 splitByC := false
@@ -71,7 +62,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	assemblingFeature := "VDJRegion" // Hardcoded to VDJRegion
 	splitByC := false
 
-	productiveFeature := "VDJRegionInFrame"
+	productiveFeature := "VDJRegion"
 	coreGeneFeatures := {
 		V: "{FR1Begin:FR3End}",
 		J: "FR4"
@@ -306,8 +297,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	annotationTypes := ["CDRs", "Segments"]
 
 	inFrameFeatures := {
-		"FR4": "FR4InFrame",
-		"VDJRegion": "VDJRegionInFrame"
+		"FR4": "FR4",
+		"VDJRegion": "VDJRegion"
 	}
 
 	for featureU in features {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.9.0",
+  "version": "1.10.1",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {

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

@@ -11,15 +11,6 @@ a := func(order, defaultVisibility, spec) {
 	})
 }
 
-/**
- * Mapping from original featuers to their in-frame variants when available.
- * This is used to avoid showing non-informative features in the clonotype browser.
- */
-inFrameFeatures := {
-	"FR4": "FR4InFrame",
-	"VDJRegion": "VDJRegionInFrame"
-}
-
 annotationMappings := {
 	"CDRs": "{\"1\":\"CDR1\",\"2\":\"CDR2\",\"3\":\"CDR3\"}",
 	"Segments": "{\"1\":\"V\",\"2\":\"D\",\"3\":\"J\",\"4\":\"C\"}"
@@ -47,7 +38,7 @@ toCombinedDomainValue := func(spec) {
  *     - J: formatted identifier for the J gene core feature (if applicable)
  */
 assemblingFeature := "VDJRegion"
-productiveFeature := "VDJRegionInFrame"
+productiveFeature := "VDJRegion"
 coreVFeature := "{FR1Begin:FR3End}"
 coreJFeature := "FR4"
 splitByC := false
@@ -71,7 +62,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	assemblingFeature := "VDJRegion" // Hardcoded to VDJRegion
 	splitByC := false
 
-	productiveFeature := "VDJRegionInFrame"
+	productiveFeature := "VDJRegion"
 	coreGeneFeatures := {
 		V: "{FR1Begin:FR3End}",
 		J: "FR4"
@@ -306,8 +297,8 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	annotationTypes := ["CDRs", "Segments"]
 
 	inFrameFeatures := {
-		"FR4": "FR4InFrame",
-		"VDJRegion": "VDJRegionInFrame"
+		"FR4": "FR4",
+		"VDJRegion": "VDJRegion"
 	}
 
 	for featureU in features {

package/src/main.tpl.tengo

@@ -22,12 +22,10 @@ wf.prepare(func(args){
 wf.body(func(args) {
 	blockId := wf.blockId().getDataAsJson()
 
-	inputRef := args.input
+	inputRef := args.datasetRef
 
 	input := wf.resolve(inputRef)
 
-	threePrimePrimer := args.threePrimePrimer
-	fivePrimePrimer := args.fivePrimePrimer
 	chains := args.chains
 	limitInput := args.limitInput
 	perProcessMemGB := args.perProcessMemGB
@@ -86,13 +84,10 @@ wf.body(func(args) {
 			blockId: blockId,
 			perProcessMemGB: perProcessMemGB,
 			perProcessCPUs: perProcessCPUs,
-			threePrimePrimer: threePrimePrimer,
-			fivePrimePrimer: fivePrimePrimer,
 			chains: chains,
 			mixcrChains: chainInfos[chains].mixcrFilter,
 			cloneClusteringMode: cloneClusteringMode,
-			hasUMI: args.hasUMI,
-			fullPattern: args.fullPattern
+			tagPattern: args.tagPattern
 		})
 	})
 

package/src/mixcr-analyze.tpl.tengo

@@ -78,16 +78,12 @@ self.body(func(inputs) {
 		arg("--rigid-right-alignment-boundary").arg("J")
 
 	// Pass pattern if provided
-	if !is_undefined(params.fullPattern) && params.fullPattern != "" {
-		if !is_undefined(params.hasUMI) && params.hasUMI {
-			mixcrCmdBuilder.arg("--tag-pattern").arg(params.fullPattern)
-		} else {
-			mixcrCmdBuilder.arg("--tag-pattern").arg(params.fullPattern)
-		}
+	if !is_undefined(params.tagPattern) && params.tagPattern != "" {
+		mixcrCmdBuilder.arg("--tag-pattern").arg(params.tagPattern)
 	}
 
 	// Clone clustering tuning
-	if cloneClusteringMode == "decrease" {
+	if cloneClusteringMode == "relaxed" {
 		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters.searchParameters=oneMismatchOrIndel")
 	} else if cloneClusteringMode == "off" {
 		mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.cloneClusteringParameters=null")

package/src/process.tpl.tengo

@@ -27,17 +27,12 @@ self.body(func(inputs) {
 	params := inputs.params
 	blockId := params.blockId
 	referenceLibrary := inputs.referenceLibrary
-	threePrimePrimer := params.threePrimePrimer
-	fivePrimePrimer := params.fivePrimePrimer
 	chains := params.chains
 	mixcrChains := params.mixcrChains
 	cloneClusteringMode := params.cloneClusteringMode
-	hasUMI := params.hasUMI
-	fullPattern := params.fullPattern
+	tagPattern := params.tagPattern
 
-	// Normalize optional params to avoid undefined in JSON
-	hasUmiBool := !is_undefined(hasUMI) && hasUMI
-	fullPatternStr := is_undefined(fullPattern) ? "" : fullPattern
+	hasUMI := text.contains(tagPattern, "UMI") || text.contains(tagPattern, "Umi") || text.contains(tagPattern, "umi")
 	limitInput := inputs.limitInput
 	perProcessMemGB := params.perProcessMemGB
 	perProcessCPUs := params.perProcessCPUs
@@ -47,7 +42,7 @@ self.body(func(inputs) {
 	presetSpecForBack := {
 		assemblingFeature: ["VDJRegion"],
 		splitByC: true,
-		umiTags: hasUmiBool ? ["Molecule"] : undefined,
+		umiTags: hasUMI ? ["Molecule"] : undefined,
 		cellTags: undefined
 	}
 
@@ -169,8 +164,8 @@ self.body(func(inputs) {
 					fileExtension: fileExtension,
 					referenceLibrary: referenceLibrary,
 					cloneClusteringMode: cloneClusteringMode,
-					hasUMI: hasUmiBool,
-					fullPattern: fullPatternStr
+					hasUMI: hasUMI,
+					tagPattern: tagPattern
 				},
 				limitInput: limitInput
 			},

package/src/wf.test.ts

@@ -1,16 +0,0 @@
-import { tplTest } from "@platforma-sdk/test";
-
-tplTest(
-  'should return a concatenated string',
-  async ({ helper, expect }) => {
-    const results = await helper.renderWorkflow("main", false, {
-      name: 'World'
-    });
-
-    const pythonMessage = results.output("pythonMessage", (a) => a?.getDataAsString());
-    expect(await pythonMessage.awaitStableValue()).eq('Hello from Python, World!\n');
-
-    const tengoMessage = results.output("tengoMessage", (a) => a?.getDataAsJson<string>());
-    expect(await tengoMessage.awaitStableValue()).eq('Hello from Tengo, World!');
-  }
-);