@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.0.1 → 2.1.0

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...

package/.turbo/turbo-test.log

@@ -1,20 +1,20 @@
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.0 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) 47946ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11920ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 7407ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7323ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7314ms
-   ✓ checking preset for 'rna-seq' 6897ms
-   ✓ checking preset for 'generic-single-cell-gex' 7083ms
+ ✓ src/test/columns.test.ts (6 tests) 48155ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11939ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 7604ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7330ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7316ms
+   ✓ checking preset for 'rna-seq' 6894ms
+   ✓ checking preset for 'generic-single-cell-gex' 7071ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  11:38:19
-   Duration  48.72s (transform 43ms, setup 0ms, collect 544ms, tests 47.95s, environment 0ms, prepare 72ms)
+   Start at  20:11:15
+   Duration  48.92s (transform 45ms, setup 0ms, collect 537ms, tests 48.16s, environment 0ms, prepare 61ms)
 

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.1.0
+
+### Minor Changes
+
+- a168fe3: pl7.app/abundance/isPrimary and pl7.app/isAnchor annotations added to the output columns
+
 ## 2.0.1
 
 ### Patch Changes

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

@@ -118,6 +118,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -134,6 +135,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -157,6 +159,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Number of UMI"
 					})
 				}
@@ -173,6 +176,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Fraction of UMI"
 					})
 				}
@@ -229,13 +233,19 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 
 
+
+	anchorFeature := undefined;
+
 	features := undefined
 	if is_undefined(assemblingFeature) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
 		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
+		anchorFeature = "CDR3"
 	}
 
 	for isImputed in ( is_undefined(assemblingFeature) ? [false, true] : [false] ) {
@@ -248,6 +258,13 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
+				annotations :=  {
+					"pl7.app/vdj/imputed": string(isImputed),
+					"pl7.app/label": featureU + " " + alphabetShort
+				}
+				if featureU == anchorFeature && !isImputed && !isAminoAcid {
+					annotations["pl7.app/isAnchor"] = "true"
+				}
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -259,10 +276,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, {
-								"pl7.app/vdj/imputed": string(isImputed),
-								"pl7.app/label": featureU + " " + alphabetShort
-							})
+							annotations: a(orderP, visibility, annotations)
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.0.1",
+  "version": "2.1.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder": "1.0.1"

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

@@ -118,6 +118,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
 				"pl7.app/label": "Number Of Reads"
 			})
 		}
@@ -134,6 +135,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				"pl7.app/isAbundance": "true",
 				"pl7.app/abundance/unit": "reads",
 				"pl7.app/abundance/normalized": "true",
+				"pl7.app/abundance/isPrimary": string(!hasUmi),
 				"pl7.app/label": "Fraction of reads"
 			})
 		}
@@ -157,6 +159,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "false",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Number of UMI"
 					})
 				}
@@ -173,6 +176,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 						"pl7.app/isAbundance": "true",
 						"pl7.app/abundance/unit": "molecules",
 						"pl7.app/abundance/normalized": "true",
+						"pl7.app/abundance/isPrimary": "true",
 						"pl7.app/label": "Fraction of UMI"
 					})
 				}
@@ -229,13 +233,19 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 
 	// Sequences
 
+	// column with nucleotide sequence of this feature will be marked as anchor
+	anchorFeature := undefined;
+
 	features := undefined
 	if is_undefined(assemblingFeature) {
 		features = ["CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = "CDR3"
 	} else if assemblingFeature != "CDR3" {
 		features = [assemblingFeature, "CDR1", "FR1", "FR2", "CDR2", "FR3", "CDR3", "FR4"]
+		anchorFeature = assemblingFeature
 	} else {
 		features = ["CDR3"]
+		anchorFeature = "CDR3"
 	}
 
 	for isImputed in ( is_undefined(assemblingFeature) ? [false, true] : [false] ) {
@@ -248,6 +258,13 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 				alphabetShort := isAminoAcid ? "aa" : "nt"
 				alphabetShortMixcr := isAminoAcid ? "aa" : "n"
 				visibility := (featureU == "CDR3") || (featureU == assemblingFeature)
+				annotations :=  {
+					"pl7.app/vdj/imputed": string(isImputed),
+					"pl7.app/label": featureU + " " + alphabetShort
+				}
+				if featureU == anchorFeature && !isImputed && !isAminoAcid {
+					annotations["pl7.app/isAnchor"] = "true"
+				}
 				columnsSpecPerClonotype += [ {
 						column: alphabetShortMixcr + "Seq" + imputedU + featureU,
 						id: alphabetShortMixcr + "-seq-" + featureL + (isImputed ? "-imputed" : ""),
@@ -259,10 +276,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 								"pl7.app/vdj/feature": featureU,
 								"pl7.app/alphabet": alphabet
 							},
-							annotations: a(orderP, visibility, {
-								"pl7.app/vdj/imputed": string(isImputed),
-								"pl7.app/label": featureU + " " + alphabetShort
-							})
+							annotations: a(orderP, visibility, annotations)
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureU ] ]

package/src/main.tpl.tengo

@@ -20,7 +20,7 @@ processTpl := assets.importTemplate(":process")
 wf.setPreRun(assets.importTemplate(":prerun"))
 
 wf.prepare(func(args){
-	return{
+	return {
 		resolvedLibraryInput: wf.resolve(args.inputLibrary, { errIfMissing: false })
 	}
 })
@@ -94,6 +94,9 @@ wf.body(func(args) {
 
 	// calculating chains
 	chains := ["IGHeavy", "IGLight", "TRA", "TRB", "TRD", "TRG"]
+	if !is_undefined(args.chains) {
+		chains = args.chains
+	}
 
 	runMixcr := render.createEphemeral(processTpl, {
 		inputSpec: input.getFutureInputField("spec"),

package/src/mixcr-export.tpl.tengo

@@ -23,6 +23,7 @@ self.body(func(inputs) {
 	// Exporting clones from clns file
 
 	mixcrCmdBuilder := exec.builder().
+		inMediumQueue().
 		printErrStreamToStdout().
 		software(mixcrSw).
 		secret("MI_LICENSE", "MI_LICENSE").

package/src/process.tpl.tengo

@@ -214,6 +214,7 @@ self.body(func(inputs) {
 				name: "pl7.app/sequencing/readIndex",
 				optional: true
 			}],
+
 			// resulting aggregation axes names will be checked against supported combinations
 			// in the body template
 			passAggregationAxesNames: true,