@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.3.1 → 2.3.3

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@2.3.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.3.3 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

@@ -1,36 +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@2.3.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.3.3 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
 
-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
+ ✓ src/test/columns.test.ts (6 tests) 55337ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13201ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8799ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8762ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8478ms
+   ✓ checking preset for 'rna-seq' 8061ms
+   ✓ checking preset for 'generic-single-cell-gex' 8035ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  18:26:47
-   Duration  64.84s (transform 40ms, setup 0ms, collect 562ms, tests 64.04s, environment 0ms, prepare 66ms)
+   Start at  15:41:23
+   Duration  56.28s (transform 52ms, setup 0ms, collect 657ms, tests 55.34s, environment 0ms, prepare 77ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.3.3
+
+### Patch Changes
+
+- 675cd29: Fix for output column domains, ordering and visibility
+
+## 2.3.2
+
+### Patch Changes
+
+- 43d3a75: updated MiXCR
+
 ## 2.3.1
 
 ### Patch Changes

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

@@ -85,6 +85,9 @@ addSpec := func(columns, additionalSpec) {
 	})
 }
 
+
+
+
 calculateExportSpecs := func(presetSpecForBack, blockId) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
@@ -210,14 +213,14 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	if isSingleCell {
 
-
-
-
-
-
-
-
-
+		columnsSpecPerSample = addSpec(columnsSpecPerSample, {
+			spec: {
+				annotations: {
+					"pl7.app/abundance/isPrimary": undefined,
+					"pl7.app/isAnchor": undefined
+				}
+			}
+		})
 		columnsSpecPerSampleSc = [ {
 			column: "uniqueCellCount",
 			id: "cell-count",
@@ -225,7 +228,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueCellCount",
 				valueType: "Long",
-				annotations: a(88000, true, {
+				annotations: a(20100, true, {
 					"pl7.app/min": "1",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "cells",
@@ -242,7 +245,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueCellFraction",
 				valueType: "Double",
-				annotations: a(88000, true, {
+				annotations: a(20000, false, {
 					"pl7.app/min": "0",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "cells",
@@ -254,48 +257,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		} ]
 	}
 
-
-
 	orderP := 80000
-	geneHitColumnVariants := [ {
-			name: "pl7.app/vdj/geneHitWithAllele",
-			columnNameSuffix: "Hit",
-			idSuffix: "-hit-with-allele",
-			labelSuffix: " hit with allele",
-			argSuffix: "Hit",
-			visible: false
-		}, {
-			name: "pl7.app/vdj/geneHit",
-			columnNameSuffix: "Gene",
-			idSuffix: "-gene",
-			labelSuffix: " gene",
-			argSuffix: "Gene",
-			visible: true
-		} ]
-	for vdjcU in ["V", "D", "J", "C"] {
-		vdjcL := text.to_lower(vdjcU)
-		for variant in geneHitColumnVariants {
-			columnsSpecPerClonotype += [ {
-					column: "best" + vdjcU + variant.columnNameSuffix,
-					id: "best-" + vdjcL + variant.idSuffix,
-					naRegex: "",
-					allowNA: vdjcU == "C" || vdjcU == "D",
-					spec: {
-						name: variant.name,
-						valueType: "String",
-						domain: {
-							"pl7.app/vdj/reference": vdjcU + "Gene"
-						},
-						annotations: a(orderP, variant.visible, {
-							"pl7.app/label": "Best " + vdjcU + variant.labelSuffix,
-							"pl7.app/isDiscreteFilter": "true"
-						})
-					}
-				} ]
-			exportArgs += [ [ "-" + vdjcL + variant.argSuffix ] ]
-			orderP -= 100
-		}
-	}
 
 
 
@@ -323,7 +285,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
-				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
+				visibility := isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -370,6 +332,48 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
+	geneHitColumnVariants := [ {
+			name: "pl7.app/vdj/geneHitWithAllele",
+			columnNameSuffix: "Hit",
+			idSuffix: "-hit-with-allele",
+			labelSuffix: " hit with allele",
+			argSuffix: "Hit",
+			visible: false
+		}, {
+			name: "pl7.app/vdj/geneHit",
+			columnNameSuffix: "Gene",
+			idSuffix: "-gene",
+			labelSuffix: " gene",
+			argSuffix: "Gene",
+			visible: true
+		} ]
+	for vdjcU in ["V", "D", "J", "C"] {
+		vdjcL := text.to_lower(vdjcU)
+		for variant in geneHitColumnVariants {
+			columnsSpecPerClonotype += [ {
+					column: "best" + vdjcU + variant.columnNameSuffix,
+					id: "best-" + vdjcL + variant.idSuffix,
+					naRegex: "",
+					allowNA: vdjcU == "C" || vdjcU == "D",
+					spec: {
+						name: variant.name,
+						valueType: "String",
+						domain: {
+							"pl7.app/vdj/reference": vdjcU + "Gene"
+						},
+						annotations: a(orderP, variant.visible, {
+							"pl7.app/label": "Best " + vdjcU + variant.labelSuffix,
+							"pl7.app/isDiscreteFilter": "true"
+						})
+					}
+				} ]
+			exportArgs += [ [ "-" + vdjcL + variant.argSuffix ] ]
+			orderP -= 100
+		}
+	}
+
+
+
 	orderP = 10000
 
 	mutationColumnVariants := [ {
@@ -430,7 +434,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			specName: "pl7.app/vdj/sequence/productive",
 			label: "Productive",
 			id: "is-productive",
-			visibility: true
+			visibility: false
 		}, {
 			columnPrefix: "isOOF",
 			arg: "-isOOF",
@@ -532,6 +536,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		"pl7.app/vdj/clonotypingRunId": blockId
 	} } })
 
+	columnsSpecPerSampleSc = addSpec(columnsSpecPerSampleSc, { spec: { domain: {
+		"pl7.app/vdj/clonotypingRunId": blockId
+	} } })
+
 
 
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^3.1.0",
@@ -8,7 +8,7 @@
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.0.2",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-148-develop",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-149-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
     "@platforma-sdk/test": "^1.25.0",
     "vitest": "^2.1.8",

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

@@ -85,6 +85,9 @@ addSpec := func(columns, additionalSpec) {
 	})
 }
 
+// Ordering rules
+//   AA Sequences
+
 calculateExportSpecs := func(presetSpecForBack, blockId) {
 	ops := exportSpecOpsFromPreset(presetSpecForBack)
 
@@ -210,14 +213,14 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	if isSingleCell {
 		// copying reads and umi counts and fraction removing isPrimary and isAnchor
-		// addSpec(columnsSpecPerSample, {
-		// 	spec: {
-		// 		annotations: {
-		// 			"pl7.app/abundance/isPrimary": undefined,
-		// 			"pl7.app/isAnchor": undefined
-		// 		}
-		// 	}
-		// }) +
+		columnsSpecPerSample = addSpec(columnsSpecPerSample, {
+			spec: {
+				annotations: {
+					"pl7.app/abundance/isPrimary": undefined,
+					"pl7.app/isAnchor": undefined
+				}
+			}
+		})
 		columnsSpecPerSampleSc = [ {
 			column: "uniqueCellCount",
 			id: "cell-count",
@@ -225,7 +228,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueCellCount",
 				valueType: "Long",
-				annotations: a(88000, true, {
+				annotations: a(20100, true, {
 					"pl7.app/min": "1",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "cells",
@@ -242,7 +245,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				name: "pl7.app/vdj/uniqueCellFraction",
 				valueType: "Double",
-				annotations: a(88000, true, {
+				annotations: a(20000, false, {
 					"pl7.app/min": "0",
 					"pl7.app/isAbundance": "true",
 					"pl7.app/abundance/unit": "cells",
@@ -254,48 +257,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		} ]
 	}
 
-	// VDJC Hits
-
 	orderP := 80000
-	geneHitColumnVariants := [ {
-			name: "pl7.app/vdj/geneHitWithAllele",
-			columnNameSuffix: "Hit",
-			idSuffix: "-hit-with-allele",
-			labelSuffix: " hit with allele",
-			argSuffix: "Hit",
-			visible: false
-		}, {
-			name: "pl7.app/vdj/geneHit",
-			columnNameSuffix: "Gene",
-			idSuffix: "-gene",
-			labelSuffix: " gene",
-			argSuffix: "Gene",
-			visible: true
-		} ]
-	for vdjcU in ["V", "D", "J", "C"] {
-		vdjcL := text.to_lower(vdjcU)
-		for variant in geneHitColumnVariants {
-			columnsSpecPerClonotype += [ {
-					column: "best" + vdjcU + variant.columnNameSuffix,
-					id: "best-" + vdjcL + variant.idSuffix,
-					naRegex: "",
-					allowNA: vdjcU == "C" || vdjcU == "D",
-					spec: {
-						name: variant.name,
-						valueType: "String",
-						domain: {
-							"pl7.app/vdj/reference": vdjcU + "Gene"
-						},
-						annotations: a(orderP, variant.visible, {
-							"pl7.app/label": "Best " + vdjcU + variant.labelSuffix,
-							"pl7.app/isDiscreteFilter": "true"
-						})
-					}
-				} ]
-			exportArgs += [ [ "-" + vdjcL + variant.argSuffix ] ]
-			orderP -= 100
-		}
-	}
 
 	// Sequences
 
@@ -323,7 +285,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
-				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
+				visibility := isSingleCell ? (featureU == "CDR3") && isAminoAcid : (featureU == "CDR3") || (featureU == assemblingFeature)
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -368,6 +330,48 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		}
 	}
 
+	// VDJC Hits
+
+	geneHitColumnVariants := [ {
+			name: "pl7.app/vdj/geneHitWithAllele",
+			columnNameSuffix: "Hit",
+			idSuffix: "-hit-with-allele",
+			labelSuffix: " hit with allele",
+			argSuffix: "Hit",
+			visible: false
+		}, {
+			name: "pl7.app/vdj/geneHit",
+			columnNameSuffix: "Gene",
+			idSuffix: "-gene",
+			labelSuffix: " gene",
+			argSuffix: "Gene",
+			visible: true
+		} ]
+	for vdjcU in ["V", "D", "J", "C"] {
+		vdjcL := text.to_lower(vdjcU)
+		for variant in geneHitColumnVariants {
+			columnsSpecPerClonotype += [ {
+					column: "best" + vdjcU + variant.columnNameSuffix,
+					id: "best-" + vdjcL + variant.idSuffix,
+					naRegex: "",
+					allowNA: vdjcU == "C" || vdjcU == "D",
+					spec: {
+						name: variant.name,
+						valueType: "String",
+						domain: {
+							"pl7.app/vdj/reference": vdjcU + "Gene"
+						},
+						annotations: a(orderP, variant.visible, {
+							"pl7.app/label": "Best " + vdjcU + variant.labelSuffix,
+							"pl7.app/isDiscreteFilter": "true"
+						})
+					}
+				} ]
+			exportArgs += [ [ "-" + vdjcL + variant.argSuffix ] ]
+			orderP -= 100
+		}
+	}
+
 	// Mutations
 
 	orderP = 10000
@@ -430,7 +434,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			specName: "pl7.app/vdj/sequence/productive",
 			label: "Productive",
 			id: "is-productive",
-			visibility: true
+			visibility: false
 		}, {
 			columnPrefix: "isOOF",
 			arg: "-isOOF",
@@ -532,6 +536,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		"pl7.app/vdj/clonotypingRunId": blockId
 	} } })
 
+	columnsSpecPerSampleSc = addSpec(columnsSpecPerSampleSc, { spec: { domain: {
+		"pl7.app/vdj/clonotypingRunId": blockId
+	} } })
+
 	//   "pl7.app/segmentedBy" annotation indicates columns that can be meaningfully merged across
 	//   different runs (given they have the same name and axes signature).
 	//   Its absence indicates that merging would be semantically meaningless (e.g., abundance

package/src/process.tpl.tengo

@@ -451,7 +451,7 @@ self.body(func(inputs) {
 			for chainIdx in [0, 1] {
 				// "A" chain is always the one that is more diverse
 				chainLetterU := ["A", "B"][chainIdx]
-				chainNameU := chainInfos[receptorInfo.chains[chainIdx]].name
+				chainNameU := chainInfos[receptorInfo.chains[chainIdx]].shortName
 				chainNameL := text.to_lower(chainNameU)
 
 				for isPrimary in [true, false] {
@@ -463,12 +463,25 @@ self.body(func(inputs) {
 					// i.e. propertiesAPrimaryTsv
 					propertiesTsvOutputName := propertiesTableName + "Tsv"
 
+					annotationsTransformation := {
+						"pl7.app/label": func(label) {
+							return chainNameU + " " + label + " " + pPrefixU
+						}
+					}
+
+					if !isPrimary {
+						annotationsTransformation["pl7.app/table/visibility"] = "optional"
+					}
+
 					singleCellOutputs += [ {
 						type: "Resource",
 						spec: {
 							kind: "PColumn",
 							name: "mixcr.com/scClonotypeTable/" + chainNameL + pPrefixU,
 							domain: {
+								"pl7.app/vdj/receptor": receptor,
+								"pl7.app/vdj/scClonotypeChain": chainLetterU,
+								"pl7.app/vdj/scClonotypeChain/index": pPrefixL,
 								"pl7.app/vdj/clonotypingRunId": blockId
 							},
 							valueType: "File"
@@ -484,13 +497,10 @@ self.body(func(inputs) {
 								spec: {
 									domain: {
 										"pl7.app/vdj/receptor": receptor,
-										"pl7.app/vdj/scClonotypeChain": chainLetterU
+										"pl7.app/vdj/scClonotypeChain": chainLetterU,
+										"pl7.app/vdj/scClonotypeChain/index": pPrefixL
 									},
-									annotations: {
-										"pl7.app/label": func(label) {
-											return pPrefixU + " " + chainNameU + " " + label
-										}
-									}
+									annotations: annotationsTransformation
 								}
 							}),
 							storageFormat: "Binary",