@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.2.2 → 2.3.1

package/.turbo/turbo-build.log

@@ -1,7 +1,9 @@
+ WARN  Issue while reading "/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.2 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.3.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
+  info: Skipping unknown file type: test/columns.test.ts
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
 Processing "src/calculate-export-specs.lib.tengo"...
 Processing "src/calculate-preset-info.tpl.tengo"...
@@ -10,10 +12,12 @@ Processing "src/main.tpl.tengo"...
 Processing "src/mixcr-analyze.tpl.tengo"...
 Processing "src/mixcr-export.tpl.tengo"...
 Processing "src/prerun.tpl.tengo"...
+Processing "src/process-single-cell.tpl.tengo"...
 Processing "src/process.tpl.tengo"...
 Processing "src/test/columns-calculate.tpl.tengo"...
 Processing "src/test/columns.test.tpl.tengo"...
 No syntax errors found.
+  info: Skipping unknown file type: test/columns.test.ts
   info: Compiling 'dist'...
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
@@ -22,6 +26,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-analyze.plj.gz
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-export.plj.gz
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/prerun.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/process-single-cell.plj.gz
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/process.plj.gz
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns-calculate.plj.gz
   info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns.test.plj.gz

package/.turbo/turbo-test.log

@@ -1,20 +1,36 @@
+ WARN  Issue while reading "/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.2 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.3.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > vitest
 
 
  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 46738ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11338ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 7608ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7124ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7116ms
-   ✓ checking preset for 'rna-seq' 6691ms
-   ✓ checking preset for 'generic-single-cell-gex' 6860ms
+stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
+{
+  type: 'ok',
+  value: undefined,
+  stable: false,
+  uTag: '6c11bfb3-e54c-4d9e-93d9-04ecc8a6e3c8',
+  unstableMarker: 'field_not_resolved:exportSpecs'
+}
+
+stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
+TEST FAILED SO ALTERNATIVE ROOT IS PRESETVED IN PL: test_1743445608218_96df81f8-dd85-4a6f-9cf9-a38dbe8ceb56 (NG:0x7e)
+
+stdout | src/test/columns.test.ts > checking preset for 'milab-human-dna-xcr-7genes-multiplex'
+TEST FAILED SO ALTERNATIVE ROOT IS PRESETVED IN PL: test_1743445629470_e3d0e207-7f5d-412a-92dd-ea4d171cbb48 (NG:0x188)
+
+ ✓ src/test/columns.test.ts (6 tests) 64043ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 23412ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8462ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8304ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8239ms
+   ✓ checking preset for 'rna-seq' 7620ms
+   ✓ checking preset for 'generic-single-cell-gex' 8004ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  11:23:07
-   Duration  47.64s (transform 53ms, setup 0ms, collect 631ms, tests 46.74s, environment 0ms, prepare 85ms)
+   Start at  18:26:47
+   Duration  64.84s (transform 40ms, setup 0ms, collect 562ms, tests 64.04s, environment 0ms, prepare 66ms)
 

package/CHANGELOG.md

@@ -1,5 +1,24 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.3.1
+
+### Patch Changes
+
+- e108f59: Dependency upgrade
+- Updated dependencies [e108f59]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts@1.1.0
+
+## 2.3.0
+
+### Minor Changes
+
+- 71e5326: Full SC data suppport
+
+### Patch Changes
+
+- Updated dependencies [71e5326]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts@1.0.2
+
 ## 2.2.2
 
 ### Patch Changes

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "aggregate-by-clonotype-key" | "calculate-preset-info" | "list-presets" | "mixcr-analyze" | "mixcr-export" | "prerun" | "process" | "test.columns-calculate" | "test.columns.test" | "main";
+declare type TplName = "aggregate-by-clonotype-key" | "calculate-preset-info" | "list-presets" | "mixcr-analyze" | "mixcr-export" | "prerun" | "process-single-cell" | "process" | "test.columns-calculate" | "test.columns.test" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -5,6 +5,7 @@ module.exports = { Templates: {
   'mixcr-analyze': { type: 'from-file', path: require.resolve('./tengo/tpl/mixcr-analyze.plj.gz') },
   'mixcr-export': { type: 'from-file', path: require.resolve('./tengo/tpl/mixcr-export.plj.gz') },
   'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
+  'process-single-cell': { type: 'from-file', path: require.resolve('./tengo/tpl/process-single-cell.plj.gz') },
   'process': { type: 'from-file', path: require.resolve('./tengo/tpl/process.plj.gz') },
   'test.columns-calculate': { type: 'from-file', path: require.resolve('./tengo/tpl/test.columns-calculate.plj.gz') },
   'test.columns.test': { type: 'from-file', path: require.resolve('./tengo/tpl/test.columns.test.plj.gz') },

package/dist/index.mjs

@@ -6,6 +6,7 @@ export const Templates = {
   'mixcr-analyze': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/mixcr-analyze.plj.gz') },
   'mixcr-export': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/mixcr-export.plj.gz') },
   'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
+  'process-single-cell': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process-single-cell.plj.gz') },
   'process': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process.plj.gz') },
   'test.columns-calculate': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/test.columns-calculate.plj.gz') },
   'test.columns.test': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/test.columns.test.plj.gz') },

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

@@ -79,6 +79,12 @@ exportSpecOpsFromPreset := func(presetSpecForBack) {
 	}
 }
 
+addSpec := func(columns, additionalSpec) {
+	return slices.map(columns, func(columnSpec) {
+		return maps.deepMerge(columnSpec, additionalSpec)
+	})
+}
+
 calculateExportSpecs := func(presetSpecForBack, blockId) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
@@ -87,19 +93,30 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	hasUmi := ops.hasUmi
 	splitByC := ops.splitByC
 
+	isSingleCell := !is_undefined(cellTags) && len(cellTags) > 0
+
 	assemblingFeatureInfo := assemblingFeatureInfo(assemblingFeature)
 	productiveFeature := assemblingFeatureInfo.productiveFeature
 	coreGeneFeatures := assemblingFeatureInfo.coreGeneFeatures
 
 	clonotypeKeyColumns := undefined
-	if !is_undefined(assemblingFeature) && (is_undefined(cellTags) || len(cellTags) == 0) {
+	clonotypeKeyArgs := undefined
+	if !is_undefined(assemblingFeature) {
 		clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
+		clonotypeKeyArgs = [
+			[ "-nFeature", assemblingFeature ],
+			[ "-vGene" ],
+			[ "-jGene" ]
+		]
 		if splitByC {
 			clonotypeKeyColumns += ["bestCGene"]
+			clonotypeKeyArgs += [ [ "-cGene" ] ]
 		}
+
 	}
 
 	columnsSpecPerSample := []
+	columnsSpecPerSampleSc := undefined
 	columnsSpecPerClonotype := []
 
 
@@ -191,6 +208,52 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		mainAbundanceColumn = "uniqueMoleculeFraction"
 	}
 
+	if isSingleCell {
+
+
+
+
+
+
+
+
+
+		columnsSpecPerSampleSc = [ {
+			column: "uniqueCellCount",
+			id: "cell-count",
+			allowNA: false,
+			spec: {
+				name: "pl7.app/vdj/uniqueCellCount",
+				valueType: "Long",
+				annotations: a(88000, true, {
+					"pl7.app/min": "1",
+					"pl7.app/isAbundance": "true",
+					"pl7.app/abundance/unit": "cells",
+					"pl7.app/abundance/normalized": "false",
+					"pl7.app/abundance/isPrimary": "true",
+					"pl7.app/isAnchor": "true",
+					"pl7.app/label": "Number of Cells"
+				})
+			}
+		}, {
+			column: "uniqueCellFraction",
+			id: "cell-fraction",
+			allowNA: false,
+			spec: {
+				name: "pl7.app/vdj/uniqueCellFraction",
+				valueType: "Double",
+				annotations: a(88000, true, {
+					"pl7.app/min": "0",
+					"pl7.app/isAbundance": "true",
+					"pl7.app/abundance/unit": "cells",
+					"pl7.app/abundance/normalized": "true",
+					"pl7.app/abundance/isPrimary": "true",
+					"pl7.app/label": "Fraction of Cells"
+				})
+			}
+		} ]
+	}
+
 
 
 	orderP := 80000
@@ -310,21 +373,21 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	orderP = 10000
 
 	mutationColumnVariants := [ {
-			name: "Mutations",
-			valueType: "String",
-			labelPart: " mutations in ",
-			idPart: "-mutations-"
-		}, {
-			name: "MutationsCount",
-			valueType: "Int",
-			labelPart: " mutations count in ",
-			idPart: "-mutations-count-"
-		}, {
-			name: "MutationsRate",
-			valueType: "Double",
-			labelPart: " mutations rate in ",
-			idPart: "-mutations-rate-"
-		} ]
+		name: "Mutations",
+		valueType: "String",
+		labelPart: " mutations in ",
+		idPart: "-mutations-"
+	}, {
+		name: "MutationsCount",
+		valueType: "Int",
+		labelPart: " mutations count in ",
+		idPart: "-mutations-count-"
+	}, {
+		name: "MutationsRate",
+		valueType: "Double",
+		labelPart: " mutations rate in ",
+		idPart: "-mutations-rate-"
+	} ]
 
 	for isAminoAcid in [false, true] {
 		alphabetShort := isAminoAcid ? "AA" : "Nt"
@@ -465,12 +528,6 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
-	addSpec := func(columns, additionalSpec) {
-		return slices.map(columns, func(columnSpec) {
-			return maps.deepMerge(columnSpec, additionalSpec)
-		})
-	}
-
 	columnsSpecPerSample = addSpec(columnsSpecPerSample, { spec: { domain: {
 		"pl7.app/vdj/clonotypingRunId": blockId
 	} } })
@@ -500,10 +557,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 	axesByClonotypeKey := undefined
+	axesByScClonotypeKey := undefined
+	cellTagColumns := undefined
 
 	if !is_undefined(clonotypeKeyColumns) {
-		ll.assert(is_undefined(cellTags) || len(cellTags) == 0, "cellTags and clonotypeKeyAxes cannot both be defined")
-
 
 		keyStrincture := []
 		for keyColumn in clonotypeKeyColumns {
@@ -515,93 +572,70 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		}
 
 		axesByClonotypeKey = [ {
-				column: "clonotypeKey",
+			column: "clonotypeKey",
+			naRegex: "",
+			spec: {
+				name: "pl7.app/vdj/clonotypeKey",
+				type: "String",
+				domain: {
+					"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture))
+				},
+				annotations: {
+					"pl7.app/label": "Clonotype key",
+					"pl7.app/table/visibility": "optional",
+					"pl7.app/table/orderPriority": "110000"
+				}
+			}
+		} ]
+
+		if isSingleCell {
+			cellTagColumns = slices.map(cellTags, func(cellTag) {
+				return "tagValue" + cellTag
+			})
+
+			axesByScClonotypeKey = [ {
+				column: "scClonotypeKey",
 				naRegex: "",
 				spec: {
-					name: "pl7.app/vdj/clonotypeKey",
+					name: "pl7.app/vdj/scClonotypeKey",
 					type: "String",
 					domain: {
-						"pl7.app/vdj/clonotypeKey/structure": string(json.encode(keyStrincture))
+						"pl7.app/vdj/scClonotypeKey/structure": string(json.encode(keyStrincture))
 					},
 					annotations: {
-						"pl7.app/label": "Clonotype key",
+						"pl7.app/label": "SC Clonotype key",
 						"pl7.app/table/visibility": "optional",
 						"pl7.app/table/orderPriority": "110000"
 					}
 				}
 			} ]
-	}
 
-	axesByClonotypeId := [ {
-		column: "cloneId",
-		spec: {
-			name: "pl7.app/vdj/cloneId",
-			type: "Long",
-			domain: {
-				"pl7.app/blockId": blockId
-			},
-			annotations: {
-				"pl7.app/min": "0",
-				"pl7.app/label": "Clone id",
-				"pl7.app/table/visibility": "optional",
-				"pl7.app/table/orderPriority": "90000"
-				}
-			}
-		} ]
-	exportArgs += [ [ "-cloneId" ] ]
-
-	orderP = 100000
-	if !is_undefined(cellTags) && len(cellTags) > 0 {
-		for tag in cellTags {
-			label := undefined
-			if tag == "CELL" {
-				label = "Cell tag"
-			} else {
-				label = text.to_title(tag[:4]) + " " + text.to_lower(tag[4:])
-			}
-			axesByClonotypeId += [ {
-					column: "tagValue" + tag,
-					naRegex: "",
-					spec: {
-						name: "pl7.app/vdj/cellTag",
-						type: "String",
-						domain: {
-							"pl7.app/vdj/cellTagId": tag,
-							"pl7.app/vdj/clonotypingRunId": blockId
-						},
-						annotations: a(orderP, true, {
-							"pl7.app/label": label
-						})
-					}
-				} ]
-			orderP -= 1
-		}
-		exportArgs += [ [ "-tags", "Cell" ] ]
 
-		columnsSpec += [ {
-				column: "cellGroup",
-				id: "cell-group",
-				naRegex: "undefined|contamination",
-				allowNA: true,
-				spec: {
-					name: "pl7.app/vdj/cellGroup",
-					valueType: "Long",
-					annotations: a(24000, true, {
-						"pl7.app/min": "0",
-						"pl7.app/label": "Cell group number"
-					} )
-				}
-			} ]
-		exportArgs += [ [ "-cellGroup" ] ]
+
+
+
+
+
+
+
+
+
+
+
+		}
 	}
 
 	return {
 		clonotypeKeyColumns: clonotypeKeyColumns,
+		clonotypeKeyArgs: clonotypeKeyArgs,
+
+		cellTagColumns: cellTagColumns,
 
-		axesByClonotypeId: axesByClonotypeId,
 		axesByClonotypeKey: axesByClonotypeKey,
+		axesByScClonotypeKey: axesByScClonotypeKey,
 
 		columnsSpecPerSample: columnsSpecPerSample,
+		columnsSpecPerSampleSc: columnsSpecPerSampleSc,
 		columnsSpecPerClonotype: columnsSpecPerClonotype,
 
 		columnsSpec: columnsSpec,

package/package.json

@@ -1,18 +1,16 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.2.2",
+  "version": "2.3.1",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder": "1.0.1"
+    "@platforma-sdk/workflow-tengo": "^3.1.0",
+    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^1.19.2",
-    "@platforma-sdk/workflow-tengo": "^2.15.6",
-    "@milaboratories/software-pframes-conv": "2.1.16",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.15.16",
+    "@platforma-sdk/tengo-builder": "^2.0.2",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-148-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.22.100",
+    "@platforma-sdk/test": "^1.25.0",
     "vitest": "^2.1.8",
     "typescript": "~5.5.4"
   },