@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.6.1 → 2.8.1

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@2.6.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.1 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@2.6.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.1 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) 55868ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 14243ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8794ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8380ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8294ms
-   ✓ checking preset for 'rna-seq' 7887ms
-   ✓ checking preset for 'generic-single-cell-gex' 8268ms
+ ✓ src/test/columns.test.ts (6 tests) 52630ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12190ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8567ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8302ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8076ms
+   ✓ checking preset for 'rna-seq' 7653ms
+   ✓ checking preset for 'generic-single-cell-gex' 7842ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  16:45:12
-   Duration  56.68s (transform 41ms, setup 0ms, collect 572ms, tests 55.87s, environment 0ms, prepare 60ms)
+   Start at  15:34:37
+   Duration  53.50s (transform 48ms, setup 0ms, collect 601ms, tests 52.63s, environment 0ms, prepare 78ms)
 

package/CHANGELOG.md

@@ -1,5 +1,23 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.8.1
+
+### Patch Changes
+
+- f838dd2: Remove CDR3 length column from output
+
+## 2.8.0
+
+### Minor Changes
+
+- 22a4bd4: passing library into exportClones template
+
+## 2.7.0
+
+### Minor Changes
+
+- a3d8933: ampliseq preset bug correction
+
 ## 2.6.1
 
 ### Patch Changes

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

@@ -46,7 +46,7 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		splittedFeature := text.split(assemblingFeature, "_TO_")
 		if len(splittedFeature) == 2 {
 			if splittedFeature[1] == "FR4" {
-				productiveFeature = "{"+splittedFeature[0] + "Begin:FR4End(-1)}"
+				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
 				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {
@@ -536,38 +536,6 @@ 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

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.6.1",
+  "version": "2.8.1",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.0.3",

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

@@ -46,7 +46,7 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		splittedFeature := text.split(assemblingFeature, "_TO_")
 		if len(splittedFeature) == 2 {
 			if splittedFeature[1] == "FR4" {
-				productiveFeature = "{"+splittedFeature[0] + "Begin:FR4End(-1)}"
+				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
 				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {
@@ -535,38 +535,6 @@ 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

package/src/mixcr-export.tpl.tengo

@@ -16,6 +16,8 @@ self.body(func(inputs) {
 	clnsFile := inputs[pConstants.VALUE_FIELD_NAME]
 
 	params := inputs.params
+	library := inputs.library
+	isLibraryFileGzipped := params.isLibraryFileGzipped
 	chains := params.chains
 	exportArgs := params.exportArgs
 
@@ -37,6 +39,14 @@ self.body(func(inputs) {
 			arg("--reset-export-clone-table-splitting").
 			arg("--chains").arg(chains)
 
+		if library {
+			if isLibraryFileGzipped {
+				mixcrCmdBuilder.addFile("library.json.gz", library)
+			} else {
+				mixcrCmdBuilder.addFile("library.json", library)
+			}
+		}
+
 		additionalAction(mixcrCmdBuilder)
 
 		return mixcrCmdBuilder.

package/src/process.tpl.tengo

@@ -351,8 +351,10 @@ self.body(func(inputs) {
 						clonotypeKeyColumns: clonotypeKeyColumns,
 						clonotypeKeyArgs: clonotypeKeyArgs,
 						cellTagColumns: cellTagColumns,
-						exportArgs: exportArgs
-					}
+						exportArgs: exportArgs,
+						isLibraryFileGzipped: isLibraryFileGzipped
+					},
+					library: library
 				}
 			}
 		)