@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.5.0 → 2.5.1

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@2.5.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.5.1 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

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@2.5.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.5.1 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) 53188ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12934ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8323ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8051ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8026ms
-   ✓ checking preset for 'rna-seq' 7829ms
-   ✓ checking preset for 'generic-single-cell-gex' 8023ms
+ ✓ src/test/columns.test.ts (6 tests) 55335ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13611ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8802ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8358ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8466ms
+   ✓ checking preset for 'rna-seq' 8068ms
+   ✓ checking preset for 'generic-single-cell-gex' 8028ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  09:32:55
-   Duration  53.99s (transform 41ms, setup 0ms, collect 564ms, tests 53.19s, environment 0ms, prepare 60ms)
+   Start at  16:04:59
+   Duration  56.24s (transform 54ms, setup 0ms, collect 634ms, tests 55.34s, environment 0ms, prepare 77ms)
 

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.5.1
+
+### Patch Changes
+
+- fedc4ee: Added clonotype key label column for bulk data
+- Updated dependencies [fedc4ee]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts@1.1.1
+
 ## 2.5.0
 
 ### Minor Changes

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

@@ -285,9 +285,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				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)
 				columnsSpecPerClonotype += [ {
-						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
+						column: columnName,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
 						naRegex: "region_not_covered",
 						spec: {
@@ -303,28 +304,27 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 							})
 						}
 					} ]
-				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
-				if !isImputed && !isAminoAcid {
-					columnsSpecPerSample += [ {
-							column: "minQual" + featureU,
-							id: "min-qual-" + featureL,
-							naRegex: "region_not_covered",
-							spec: {
-								name: "pl7.app/vdj/sequenceQuality",
-								valueType: "Int",
-								domain: {
-									"pl7.app/vdj/quality": "minQuality",
-									"pl7.app/vdj/feature": featureU
-								},
-								annotations: a(orderP - 10, false, {
-									"pl7.app/min": "0",
-									"pl7.app/max": "60",
-									"pl7.app/label": "Min quality " + featureU
-								})
+
+
+				if isAminoAcid && !isSingleCell && featureU == "CDR3" {
+					columnsSpecPerClonotype += [ {
+						column: columnName,
+						id: "clonotype-label",
+						preProcess: [{
+							type: "regexpReplace",
+							pattern: "^region_not_covered$",
+							replacement: "Unlabelled"
+						}],
+						spec: {
+							name: "pl7.app/label",
+							valueType: "String",
+							annotations: {
+								"pl7.app/label": "Clone label"
 							}
-						} ]
-					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+						}
+					} ]
 				}
+				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
 				orderP -= 100
 			}
 		}
@@ -595,7 +595,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/vdj/clonotypingRunId": blockId
 					},
 					annotations: {
-						"pl7.app/label": "SC Clonotype key",
+						"pl7.app/label": "Clone label",
 						"pl7.app/table/visibility": "optional",
 						"pl7.app/table/orderPriority": "110000",
 						"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.5.0",
+  "version": "2.5.1",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^3.1.0",
-    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.0"
+    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.1"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.0.2",

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

@@ -285,9 +285,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				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)
 				columnsSpecPerClonotype += [ {
-						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
+						column: columnName,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
 						naRegex: "region_not_covered",
 						spec: {
@@ -303,28 +304,27 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 							})
 						}
 					} ]
-				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
-				if !isImputed && !isAminoAcid {
-					columnsSpecPerSample += [ {
-							column: "minQual" + featureU,
-							id: "min-qual-" + featureL,
-							naRegex: "region_not_covered",
-							spec: {
-								name: "pl7.app/vdj/sequenceQuality",
-								valueType: "Int",
-								domain: {
-									"pl7.app/vdj/quality": "minQuality",
-									"pl7.app/vdj/feature": featureU
-								},
-								annotations: a(orderP - 10, false, {
-									"pl7.app/min": "0",
-									"pl7.app/max": "60",
-									"pl7.app/label": "Min quality " + featureU
-								})
+
+				// label column
+				if isAminoAcid && !isSingleCell && featureU == "CDR3" {
+					columnsSpecPerClonotype += [ {
+						column: columnName,
+						id: "clonotype-label",
+						preProcess: [{
+							type: "regexpReplace",
+							pattern: "^region_not_covered$",
+							replacement: "Unlabelled"
+						}],
+						spec: {
+							name: "pl7.app/label",
+							valueType: "String",
+							annotations: {
+								"pl7.app/label": "Clone label"
 							}
-						} ]
-					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+						}
+					} ]
 				}
+				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]
 				orderP -= 100
 			}
 		}
@@ -595,7 +595,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/vdj/clonotypingRunId": blockId
 					},
 					annotations: {
-						"pl7.app/label": "SC Clonotype key",
+						"pl7.app/label": "Clone label",
 						"pl7.app/table/visibility": "optional",
 						"pl7.app/table/orderPriority": "110000",
 						"pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))