@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.23.3 → 3.23.5

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.3 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.5 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 3.23.5
+
+### Patch Changes
+
+- 5279399: Fix memory request for pt invocation
+
+## 3.23.4
+
+### Patch Changes
+
+- 9c08972: Update RNA-seq preset
+
 ## 3.23.3
 
 ### Patch Changes

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

@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
+	isRnaSeqPreset := is_undefined(assemblingFeature)
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	clonotypeKeyArgs := undefined
 
 	if !is_undefined(assemblingFeature) {
-		clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
-		clonotypeKeyArgs = [
-			[ "-nFeature", assemblingFeature ],
-			[ "-vGene" ],
-			[ "-jGene" ]
-		]
+		if isRnaSeqPreset {
+			clonotypeKeyColumns = [
+				"nSeqFR1",
+				"nSeqCDR1",
+				"nSeqFR2",
+				"nSeqCDR2",
+				"nSeqFR3",
+				"nSeqCDR3",
+				"bestVGene",
+				"bestJGene"
+			]
+			clonotypeKeyArgs = [
+				[ "-nFeature", "FR1" ],
+				[ "-nFeature", "CDR1" ],
+				[ "-nFeature", "FR2" ],
+				[ "-nFeature", "CDR2" ],
+				[ "-nFeature", "FR3" ],
+				[ "-nFeature", "CDR3" ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		} else {
+			clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
+			clonotypeKeyArgs = [
+				[ "-nFeature", assemblingFeature ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		}
 		if splitByC {
 			clonotypeKeyColumns += ["bestCHit"]
 			clonotypeKeyArgs += [ [ "-cHit" ] ]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.23.3",
+  "version": "3.23.5",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.8.2",

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

@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
 	assemblingFeature := ops.assemblingFeature
+	isRnaSeqPreset := is_undefined(assemblingFeature)
 	cellTags := ops.cellTags
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 	clonotypeKeyArgs := undefined
 
 	if !is_undefined(assemblingFeature) {
-		clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
-		clonotypeKeyArgs = [
-			[ "-nFeature", assemblingFeature ],
-			[ "-vGene" ],
-			[ "-jGene" ]
-		]
+		if isRnaSeqPreset {
+			clonotypeKeyColumns = [
+				"nSeqFR1",
+				"nSeqCDR1",
+				"nSeqFR2",
+				"nSeqCDR2",
+				"nSeqFR3",
+				"nSeqCDR3",
+				"bestVGene",
+				"bestJGene"
+			]
+			clonotypeKeyArgs = [
+				[ "-nFeature", "FR1" ],
+				[ "-nFeature", "CDR1" ],
+				[ "-nFeature", "FR2" ],
+				[ "-nFeature", "CDR2" ],
+				[ "-nFeature", "FR3" ],
+				[ "-nFeature", "CDR3" ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		} else {
+			clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
+			clonotypeKeyArgs = [
+				[ "-nFeature", assemblingFeature ],
+				[ "-vGene" ],
+				[ "-jGene" ]
+			]
+		}
 		if splitByC {
 			clonotypeKeyColumns += ["bestCHit"]
 			clonotypeKeyArgs += [ [ "-cHit" ] ]

package/src/mixcr-export.tpl.tengo

@@ -7,6 +7,7 @@ smart := import("@platforma-sdk/workflow-tengo:smart")
 slices := import("@platforma-sdk/workflow-tengo:slices")
 assets := import("@platforma-sdk/workflow-tengo:assets")
 exec := import("@platforma-sdk/workflow-tengo:exec")
+units := import("@platforma-sdk/workflow-tengo:units")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 clonotypeLabel := import(":clonotype-label")
 stopCodonReplacement := import(":stop-codon-replacement")
@@ -31,7 +32,7 @@ self.body(func(inputs) {
 	aminoAcidSeqColumns := params.aminoAcidSeqColumns
 	aminoAcidSeqColumnPairs := params.aminoAcidSeqColumnPairs
 	cdr3SeqColumns := params.cdr3SeqColumns
-	
+
 	clonotypeKeyColumns := params.clonotypeKeyColumns
 	clonotypeKeyArgs := params.clonotypeKeyArgs
 
@@ -49,7 +50,7 @@ self.body(func(inputs) {
 
 	useProductiveFilter := is_undefined(stopCodonTypes) || len(stopCodonTypes) == 0
 
-	exportMemGB := undefined 
+	exportMemGB := undefined
 	if !is_undefined(inputs.perProcessMemGB) {
 		exportMemGB = int(1.0*inputs.perProcessMemGB/4.0)
 		if exportMemGB < 12 {
@@ -59,8 +60,7 @@ self.body(func(inputs) {
 		exportMemGB = 12
 	}
 	ptMemGB := int(2.0*exportMemGB/3.0)
-	
-	
+
 	hashKeyDerivationExpressionPt := func(sourceColumns) {
 		return pt.concatStr(
 			slices.map(sourceColumns, func(colName) { return pt.col(colName).fillNull("") }),
@@ -130,7 +130,7 @@ self.body(func(inputs) {
 	// PTabler processing for main TSV output
 	wfMain := pt.workflow().
 		inMediumQueue().
-		mem(ptMemGB).
+		mem(ptMemGB * units.GiB).
 		cpu(2)
 
 	frameInputMap := {

package/src/test/columns.test.ts

@@ -111,6 +111,16 @@ const testCases: TestCase[] = [
       expect(config.columnsSpec.find((c: any) => c.column === 'readFraction')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'nSeqCDR3')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'aaSeqCDR3')).toBeDefined();
+      expect(config.clonotypeKeyColumns).toEqual([
+        'nSeqFR1',
+        'nSeqCDR1',
+        'nSeqFR2',
+        'nSeqCDR2',
+        'nSeqFR3',
+        'nSeqCDR3',
+        'bestVGene',
+        'bestJGene'
+      ]);
     }
   },
   {