@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.23.6 → 3.24.1

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@3.23.6 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.24.1 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
 
+## 3.24.1
+
+### Patch Changes
+
+- 2730802: Fix custom library usage
+
+## 3.24.0
+
+### Minor Changes
+
+- 34dfe5e: Add supporting cells column
+
 ## 3.23.6
 
 ### Patch Changes

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

@@ -462,7 +462,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 				})
 			}
 		} ]
-		columnsSpecPerClonotypeSc = [ sampleCountColumn, clonotypeLabelColumn ]
+		columnsSpecPerClonotypeSc = [
+			{
+				column: "uniqueCellCountTotal",
+				id: "cell-count-total",
+				allowNA: false,
+				spec: {
+					name: "pl7.app/vdj/uniqueCellCountTotal",
+					valueType: "Long",
+					annotations: a(87120, true, {
+						"pl7.app/min": "1",
+						"pl7.app/isAbundance": "true",
+						"pl7.app/abundance/unit": "cells",
+						"pl7.app/abundance/normalized": "false",
+						"pl7.app/label": "Supporting Cells",
+						"pl7.app/description": "The sum of a clonotype's cell counts across all samples."
+					})
+				}
+			}, 
+		sampleCountColumn,
+		clonotypeLabelColumn
+		]
 	}
 
 	orderP := 80000

package/package.json

@@ -1,13 +1,13 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.23.6",
+  "version": "3.24.1",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.8.2",
+    "@platforma-sdk/workflow-tengo": "5.9.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-302-develop"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.18"
+    "@platforma-sdk/tengo-builder": "2.4.25"
   },
   "scripts": {
     "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",

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

@@ -462,7 +462,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
 				})
 			}
 		} ]
-		columnsSpecPerClonotypeSc = [ sampleCountColumn, clonotypeLabelColumn ]
+		columnsSpecPerClonotypeSc = [
+			{
+				column: "uniqueCellCountTotal",
+				id: "cell-count-total",
+				allowNA: false,
+				spec: {
+					name: "pl7.app/vdj/uniqueCellCountTotal",
+					valueType: "Long",
+					annotations: a(87120, true, {
+						"pl7.app/min": "1",
+						"pl7.app/isAbundance": "true",
+						"pl7.app/abundance/unit": "cells",
+						"pl7.app/abundance/normalized": "false",
+						"pl7.app/label": "Supporting Cells",
+						"pl7.app/description": "The sum of a clonotype's cell counts across all samples."
+					})
+				}
+			}, 
+		sampleCountColumn,
+		clonotypeLabelColumn
+		]
 	}
 
 	orderP := 80000

package/src/export-report.tpl.tengo

@@ -290,6 +290,13 @@ self.body(func(inputs) {
                     arg("--drop-default-fields").
                     arg("--reset-export-clone-table-splitting").
                     arg("--chains").arg(chainMixcr)
+                if library {
+                    if isLibraryFileGzipped {
+                        exportChainFiltersCmd.addFile("library.json.gz", library)
+                    } else {
+                        exportChainFiltersCmd.addFile("library.json", library)
+                    }
+                }
                 exportChainFiltersResult := exportChainFiltersCmd.
                     arg("-isOOF").arg(featureForFlags).
                     arg("-hasStops").arg(featureForFlags).

package/src/mixcr-export.tpl.tengo

@@ -203,7 +203,7 @@ self.body(func(inputs) {
 		// PTabler processing for single-cell TSV output
 		wfSingleCell := pt.workflow().
 			inMediumQueue().
-			mem(ptMemGB).
+			mem(ptMemGB * units.GiB).
 			cpu(2)
 
 		frameLoadOps := {

package/src/process-single-cell.tpl.tengo

@@ -198,7 +198,8 @@ self.body(func(inputs) {
 	clonotypeTableDf := allChainsFilteredDf.groupBy(
 		"scClonotypeKey", "clonotypeKeyA1", "clonotypeKeyA2", "clonotypeKeyB1", "clonotypeKeyB2"
 	).agg(
-		pt.col("sampleId").nUnique().alias("sampleCount")
+		pt.col("sampleId").nUnique().alias("sampleCount"),
+		pt.col("cellKey").count().alias("uniqueCellCountTotal")
 	)
 
 	clonotypeTableDf = clonotypeLabel.addClonotypeLabelColumnsPt(clonotypeTableDf, "scClonotypeKey", "clonotypeLabel", pt)
@@ -239,7 +240,8 @@ self.body(func(inputs) {
 		{ column: "clonotypeKeyA2", type: "String" },
 		{ column: "clonotypeKeyB1", type: "String" },
 		{ column: "clonotypeKeyB2", type: "String" },
-		{ column: "sampleCount", type: "Int" }
+		{ column: "sampleCount", type: "Int" },
+		{ column: "uniqueCellCountTotal", type: "Long" }
 	]
 
 	mainClonotypesDf := outputProcessingWf.frame(clonotypeTsv, {

package/src/test/columns.test.ts

@@ -1,5 +1,5 @@
 import { ImportFileHandle } from '@platforma-sdk/model';
-import { awaitStableState, tplTest, ML } from '@platforma-sdk/test';
+import { awaitStableState, ML, tplTest } from '@platforma-sdk/test';
 import { ExpectStatic } from 'vitest';
 
 type Preset =
@@ -46,6 +46,7 @@ const testCases: TestCase[] = [
       // expect(config.columnsSpec.find((c: any) => c.column === 'cellGroup')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'uniqueMoleculeCount')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'uniqueMoleculeFraction')).toBeDefined();
+      expect(config.columnsSpecPerClonotypeSc.find((c: any) => c.column === 'uniqueCellCountTotal')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'nSeqFR1')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'nSeqCDR1')).toBeDefined();
       expect(config.columnsSpec.find((c: any) => c.column === 'nSeqFR2')).toBeDefined();