@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.8.0 → 2.8.2

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  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@2.8.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.2 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

package/.turbo/turbo-test.log

@@ -1,21 +1,21 @@
  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@2.8.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.2 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) 54112ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12976ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8593ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8350ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8290ms
-   ✓ checking preset for 'rna-seq' 7833ms
-   ✓ checking preset for 'generic-single-cell-gex' 8069ms
+ ✓ src/test/columns.test.ts (6 tests) 53957ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12559ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8530ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8433ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8412ms
+   ✓ checking preset for 'rna-seq' 8008ms
+   ✓ checking preset for 'generic-single-cell-gex' 8014ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  15:43:44
-   Duration  55.17s (transform 63ms, setup 0ms, collect 737ms, tests 54.11s, environment 0ms, prepare 92ms)
+   Start at  16:34:49
+   Duration  54.77s (transform 44ms, setup 0ms, collect 587ms, tests 53.96s, environment 0ms, prepare 62ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.8.2
+
+### Patch Changes
+
+- e84b4df: SDK upgrade to fix empty tables issues & minor corrections to column generation logic
+
+## 2.8.1
+
+### Patch Changes
+
+- f838dd2: Remove CDR3 length column from output
+
 ## 2.8.0
 
 ### Minor Changes

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

@@ -269,7 +269,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
 		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
-		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4", assemblingFeature]
 		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
@@ -281,12 +281,12 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		imputedL := text.to_lower(imputedU)
 		for featureU in features {
 			featureL := text.to_lower(featureU)
-			for isAminoAcid in [false, true] {
+			for isAminoAcid in [true, false] {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				columnName := alphabetShortMixcr + "Seq" + imputedU + featureU
-				visibility := isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
+				visibility := featureU == "CDR3" && (!isSingleCell || isAminoAcid) // isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
 				columnsSpecPerClonotype += [ {
 						column: columnName,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -304,6 +304,29 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 							})
 						}
 					} ]
+				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
+				orderP -= 100
+
+
+				if featureU == "CDR3" {
+					columnsSpecPerClonotype += [ {
+						column: alphabetShortMixcr + "Length" + featureU,
+						id: alphabetShortMixcr + "-length-" + featureL,
+						naRegex: "region_not_covered",
+						spec: {
+							name: "pl7.app/vdj/sequenceLength",
+							valueType: "Int",
+							domain: {
+								"pl7.app/vdj/feature": featureU,
+								"pl7.app/alphabet": alphabet
+							},
+							annotations: a(orderP, false, {
+								"pl7.app/label": "Length of " + featureU + " " + alphabetShort
+							})
+						}
+					} ]
+					exportArgs += [ [ "-" + alphabetShortMixcr + "Length", featureU ] ]
+				}
 
 
 				if isAminoAcid && !isSingleCell && featureU == "CDR3" {
@@ -318,14 +341,12 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						spec: {
 							name: "pl7.app/label",
 							valueType: "String",
-							annotations: {
+							annotations: a(100000, false, {
 								"pl7.app/label": "Clone label"
-							}
+							})
 						}
 					} ]
 				}
-				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
-				orderP -= 100
 			}
 		}
 	}
@@ -376,7 +397,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	orderP = 10000
 
-	mutationColumnVariants := [ 
+	mutationColumnVariants := [
 
 
 
@@ -536,38 +557,6 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	]
 
 
-	
-
-	lengthColumns := ["CDR3"] // assemblingFeatureInfo.nonImputed
-
-	for featureU in lengthColumns {
-		featureL := text.to_lower(featureU)
-		for isAminoAcid in [false, true] {
-			alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
-			alphabetShort := isAminoAcid ? "aa" : "nt"
-			alphabetShortMixcr := isAminoAcid ? "aa" : "n"
-			columnsSpecPerClonotype += [ {
-				column: alphabetShortMixcr + "Length" + featureU,
-				id: alphabetShortMixcr + "-length-" + featureL,
-				naRegex: "region_not_covered",
-				spec: {
-					name: "pl7.app/vdj/sequenceLength",
-					valueType: "Int",
-					domain: {
-						"pl7.app/vdj/feature": featureU,
-						"pl7.app/alphabet": alphabet
-					},
-					annotations: a(orderP, false, {
-						"pl7.app/label": "Length of " + featureU + " " + alphabetShort
-					})
-				}
-			} ]
-			exportArgs += [ [ "-" + alphabetShortMixcr + "Length", featureU ] ]
-			orderP -= 100
-		}
-	}
-
-
 
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype
 

package/package.json

@@ -1,16 +1,16 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.8.0",
+  "version": "2.8.2",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.0.3",
+    "@platforma-sdk/workflow-tengo": "^4.0.8",
     "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.1"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.0.3",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-149-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.28.2",
+    "@platforma-sdk/test": "^1.29.3",
     "vitest": "^2.1.8",
     "typescript": "~5.5.4"
   },

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

@@ -269,7 +269,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
 		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
-		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4", assemblingFeature]
 		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
@@ -281,12 +281,12 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		imputedL := text.to_lower(imputedU)
 		for featureU in features {
 			featureL := text.to_lower(featureU)
-			for isAminoAcid in [false, true] {
+			for isAminoAcid in [true, false] {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				columnName := alphabetShortMixcr + "Seq" + imputedU + featureU
-				visibility := isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
+				visibility := featureU == "CDR3" && (!isSingleCell || isAminoAcid) // isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
 				columnsSpecPerClonotype += [ {
 						column: columnName,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -304,6 +304,29 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 							})
 						}
 					} ]
+				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
+				orderP -= 100
+
+				// For now calculate length only for CDR3 to keep the number of columns manageable
+				if featureU == "CDR3" {
+					columnsSpecPerClonotype += [ {
+						column: alphabetShortMixcr + "Length" + featureU,
+						id: alphabetShortMixcr + "-length-" + featureL,
+						naRegex: "region_not_covered",
+						spec: {
+							name: "pl7.app/vdj/sequenceLength",
+							valueType: "Int",
+							domain: {
+								"pl7.app/vdj/feature": featureU,
+								"pl7.app/alphabet": alphabet
+							},
+							annotations: a(orderP, false, {
+								"pl7.app/label": "Length of " + featureU + " " + alphabetShort
+							})
+						}
+					} ]
+					exportArgs += [ [ "-" + alphabetShortMixcr + "Length", featureU ] ]
+				}
 
 				// label column
 				if isAminoAcid && !isSingleCell && featureU == "CDR3" {
@@ -318,14 +341,12 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						spec: {
 							name: "pl7.app/label",
 							valueType: "String",
-							annotations: {
+							annotations: a(100000, false, {
 								"pl7.app/label": "Clone label"
-							}
+							})
 						}
 					} ]
 				}
-				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
-				orderP -= 100
 			}
 		}
 	}
@@ -376,7 +397,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	orderP = 10000
 
-	mutationColumnVariants := [ 
+	mutationColumnVariants := [
 	// {
 	// 	name: "Mutations",
 	// 	valueType: "String",
@@ -535,38 +556,6 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		[ "-topChains" ]
 	]
 
-	//Sequence length
-	
-	// for now use only CDR3 length to avoid generating too many columns
-	lengthColumns := ["CDR3"] // assemblingFeatureInfo.nonImputed
-
-	for featureU in lengthColumns {
-		featureL := text.to_lower(featureU)
-		for isAminoAcid in [false, true] {
-			alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
-			alphabetShort := isAminoAcid ? "aa" : "nt"
-			alphabetShortMixcr := isAminoAcid ? "aa" : "n"
-			columnsSpecPerClonotype += [ {
-				column: alphabetShortMixcr + "Length" + featureU,
-				id: alphabetShortMixcr + "-length-" + featureL,
-				naRegex: "region_not_covered",
-				spec: {
-					name: "pl7.app/vdj/sequenceLength",
-					valueType: "Int",
-					domain: {
-						"pl7.app/vdj/feature": featureU,
-						"pl7.app/alphabet": alphabet
-					},
-					annotations: a(orderP, false, {
-						"pl7.app/label": "Length of " + featureU + " " + alphabetShort
-					})
-				}
-			} ]
-			exportArgs += [ [ "-" + alphabetShortMixcr + "Length", featureU ] ]
-			orderP -= 100
-		}
-	}
-
 	// All columns are added
 
 	columnsSpec := columnsSpecPerSample + columnsSpecPerClonotype