@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.20.0 → 1.20.1

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.20.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.20.1 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/aggregate-by-clonotype-key.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.20.1
+
+### Patch Changes
+
+- fb02889: Removed all logic and dependencies related to \`cdr3Sequences\` from the \`mixcr-amplicon-alignment\` block.
+
 ## 1.20.0
 
 ### Minor Changes

package/package.json

@@ -1,13 +1,12 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.20.0",
+  "version": "1.20.1",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.8.2",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-309-develop",
-    "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master",
-    "@platforma-open/milaboratories.mixcr-amplicon-alignment.software": "1.2.0"
+    "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.4.17"

package/src/aggregate-by-clonotype-key.tpl.tengo

@@ -12,9 +12,7 @@ clonotypeLabel := import(":clonotype-label")
 math := import("math")
 json := import("json")
 
-self.defineOutputs("tsv", "cdr3DistancesTsv")
-
-cdr3DistanceSw := assets.importSoftware("@platforma-open/milaboratories.mixcr-amplicon-alignment.software:cdr3-distance-calculation")
+self.defineOutputs("tsv")
 
 self.body(func(inputs) {
 	inputData := inputs[pConstants.VALUE_FIELD_NAME]
@@ -115,37 +113,13 @@ self.body(func(inputs) {
 
 	aggregatedDf = clonotypeLabel.addClonotypeLabelColumnsPt(aggregatedDf, "clonotypeKey", "clonotypeLabel", pt)
 
-	cdr3Df := aggregatedDf.select(
-		pt.col("clonotypeKey"),
-		pt.col("nSeqCDR3").alias("nSeqCDR3"),
-		pt.col("aaSeqCDR3").alias("aaSeqCDR3")
-	)
-
 	aggregatedDf.save("output.tsv")
-	cdr3Df.save("cdr3-sequences.tsv")
 
 	ptablerResult := wf.run()
 
 	processedTsv := ptablerResult.getFile("output.tsv")
-	cdr3Tsv := ptablerResult.getFile("cdr3-sequences.tsv")
-	cdr3DistancesTsv := undefined
-
-	if !is_undefined(params.cdr3Sequences) {
-		cdr3DistanceCmd := exec.builder().
-			software(cdr3DistanceSw).
-			mem("8GB").
-			cpu(1).
-			writeFile("cdr3-sequences.fasta", params.cdr3Sequences).saveFile("cdr3-sequences.fasta").
-			arg("--tsv").arg("cdr3-sequences.tsv").addFile("cdr3-sequences.tsv", cdr3Tsv).
-			arg("--ref-fasta").arg("cdr3-sequences.fasta").
-			arg("--out").arg("cdr3-distances.tsv").saveFile("cdr3-distances.tsv")
-
-		cdr3DistanceResult := cdr3DistanceCmd.run()
-		cdr3DistancesTsv = cdr3DistanceResult.getFile("cdr3-distances.tsv")
-	}
 
 	return {
-		tsv: processedTsv,
-		cdr3DistancesTsv: cdr3DistancesTsv
+		tsv: processedTsv
 	}
 }) 

package/src/main.tpl.tengo

@@ -67,7 +67,6 @@ wf.body(func(args) {
 		inputData: input.getFutureInputField("data"),
 		referenceLibrary: referenceLibrary,
 		limitInput: limitInput,
-		cdr3Sequences: args.cdr3Sequences,
 
 		params: smart.createJsonResource(maps.clone({
 			blockId: blockId,

package/src/process.tpl.tengo

@@ -99,7 +99,6 @@ self.body(func(inputs) {
 	columnsSpecPerSample := exportSpecs.columnsSpecPerSample
 	columnsSpecPerClonotypeNoAggregates := exportSpecs.columnsSpecPerClonotypeNoAggregates
 	columnsSpecPerClonotypeAggregates := exportSpecs.columnsSpecPerClonotypeAggregates
-	cdr3DistanceColumnsSpec := exportSpecs.cdr3DistanceColumnsSpec
 	clonotypeKeyColumns := exportSpecs.clonotypeKeyColumns
 	clonotypeKeyArgs := exportSpecs.clonotypeKeyArgs
 	exportArgs := exportSpecs.exportArgs
@@ -322,18 +321,6 @@ self.body(func(inputs) {
 		cpu: 2,
 		name: "aggregates",
 		path: ["tsv"]
-	}, {
-		type: "Xsv",
-		xsvType: "tsv",
-		settings: {
-			axes: axesByClonotypeKeyWithChain,
-			columns: cdr3DistanceColumnsSpec,
-			storageFormat: "Parquet"
-		},
-		mem: memGB(8, 8),
-		cpu: 1,
-		name: "cdr3Distances",
-		path: ["cdr3DistancesTsv"]
 	} ]
 
 	aggregationResults := pframes.processColumn(
@@ -350,9 +337,7 @@ self.body(func(inputs) {
 					mainAbundanceColumnUnnormalized: mainAbundanceColumnUnnormalized,
 					schemaPerClonotypeNoAggregates: columnsToSchema(columnsSpecPerClonotypeNoAggregates),
 					schemaPerClonotypeAggregates: columnsToSchema(columnsSpecPerClonotypeAggregates),
-					schemaPerSample: columnsToSchema(columnsSpecPerSample),
-					cdr3Sequences: inputs.cdr3Sequences,
-					cdr3DistanceColumnsSpec: cdr3DistanceColumnsSpec
+					schemaPerSample: columnsToSchema(columnsSpecPerSample)
 				}
 			}
 		}
@@ -362,7 +347,6 @@ self.body(func(inputs) {
 	clones := pframes.pFrameBuilder()
 	exportResults.addXsvOutputToBuilder(clones, "byCloneKeyBySample", "clonotypeProperties/bySample/" + chains + "/")
 	aggregationResults.addXsvOutputToBuilder(clones, "aggregates", "clonotypeProperties/aggregates/" + chains + "/")
-	aggregationResults.addXsvOutputToBuilder(clones, "cdr3Distances", "clonotypeProperties/cdr3Distances/" + chains + "/")
 
 	qcReportTable := render.create(exportReportTpl, {
 		clnsData: mixcrResults.outputData("clns"),