@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.20.1 → 1.21.0

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@1.20.1 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.0 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"...
@@ -10,6 +10,7 @@ Processing "src/export-report.tpl.tengo"...
 Processing "src/main.tpl.tengo"...
 Processing "src/mixcr-analyze.tpl.tengo"...
 Processing "src/mixcr-export.tpl.tengo"...
+Processing "src/prerun.tpl.tengo"...
 Processing "src/process.tpl.tengo"...
 Processing "src/qc-report-columns.lib.tengo"...
 Processing "src/repseqio-library.tpl.tengo"...
@@ -24,6 +25,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/tpl/mixcr-export.plj.gz
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/tpl/process.plj.gz
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/tpl/repseqio-library.plj.gz
+  info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/tpl/prerun.plj.gz
   info:   - writing /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow/dist/tengo/tpl/main.plj.gz
   info: Template Pack build done.
   info: Template Pack build done.

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.21.0
+
+### Minor Changes
+
+- 00ded91: Support custom reference library
+
 ## 1.20.1
 
 ### Patch Changes

package/dist/index.cjs

@@ -5,5 +5,6 @@ module.exports = { Templates: {
   'mixcr-export': { type: 'from-file', path: require.resolve('./tengo/tpl/mixcr-export.plj.gz') },
   'process': { type: 'from-file', path: require.resolve('./tengo/tpl/process.plj.gz') },
   'repseqio-library': { type: 'from-file', path: require.resolve('./tengo/tpl/repseqio-library.plj.gz') },
+  'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
 }};

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "aggregate-by-clonotype-key" | "export-report" | "mixcr-analyze" | "mixcr-export" | "process" | "repseqio-library" | "main";
+declare type TplName = "aggregate-by-clonotype-key" | "export-report" | "mixcr-analyze" | "mixcr-export" | "process" | "repseqio-library" | "prerun" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -6,5 +6,6 @@ export const Templates = {
   'mixcr-export': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/mixcr-export.plj.gz') },
   'process': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process.plj.gz') },
   'repseqio-library': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/repseqio-library.plj.gz') },
+  'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.20.1",
+  "version": "1.21.0",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {

package/src/export-report.tpl.tengo

@@ -137,7 +137,9 @@ self.body(func(inputs) {
 
     exportReportCmd.arg("qc-report.tsv").saveFile("qc-report.tsv")
     if library {
-        if isLibraryFileGzipped {
+        if is_string(library) {
+			exportReportCmd.writeFile("library.json", library).saveFile("library.json")
+		} else if isLibraryFileGzipped {
 			exportReportCmd.addFile("library.json.gz", library)
 		} else {
 			exportReportCmd.addFile("library.json", library)
@@ -226,7 +228,9 @@ self.body(func(inputs) {
 			arg("clones.tsv").
 			saveFile("clones.tsv")
 		if library {
-			if isLibraryFileGzipped {
+			if is_string(library) {
+				exportFiltersCmd.writeFile("library.json", library).saveFile("library.json")
+			} else if isLibraryFileGzipped {
 				exportFiltersCmd.addFile("library.json.gz", library)
 			} else {
 				exportFiltersCmd.addFile("library.json", library)

package/src/main.tpl.tengo

@@ -15,6 +15,8 @@ json := import("json")
 processTpl := assets.importTemplate(":process")
 repseqioLibraryTpl := assets.importTemplate(":repseqio-library")
 
+wf.setPreRun(assets.importTemplate(":prerun"))
+
 wf.prepare(func(args){
 	return {}
 })
@@ -47,11 +49,74 @@ wf.body(func(args) {
 	debugOutput := undefined
 	libraryImportHandle := undefined
 
-	if !is_undefined(args.libraryFile) {
+	mode := args.referenceInputMode
+	if is_undefined(mode) {
+		mode = "fastaSequence"
+	}
+
+	if mode == "buildLibrary" {
+		// Build library mode — construct library.json from entry definitions
+		chainInfoForMixcr := chainInfos[chains].mixcrFilter
+		genes := []
+		fragments := []
+		for entry in args.libraryEntries {
+			vName := entry.name + "_Vgene"
+			jName := entry.name + "_Jgene"
+			vUri := "local://" + vName
+			jUri := "local://" + jName
+			genes = append(genes, {
+				baseSequence: vUri,
+				name: vName,
+				geneType: "V",
+				isFunctional: true,
+				chains: [chainInfoForMixcr],
+				anchorPoints: {
+					FR1Begin: entry.vAnchorPoints.fr1Begin,
+					CDR1Begin: entry.vAnchorPoints.cdr1Begin,
+					FR2Begin: entry.vAnchorPoints.fr2Begin,
+					CDR2Begin: entry.vAnchorPoints.cdr2Begin,
+					FR3Begin: entry.vAnchorPoints.fr3Begin,
+					CDR3Begin: entry.vAnchorPoints.cdr3Begin,
+					VEnd: entry.vAnchorPoints.vEnd
+				}
+			})
+			fragments = append(fragments, {
+				uri: vUri,
+				range: { from: 0, to: len(entry.vSequence) },
+				sequence: entry.vSequence
+			})
+			genes = append(genes, {
+				baseSequence: jUri,
+				name: jName,
+				geneType: "J",
+				isFunctional: true,
+				chains: [chainInfoForMixcr],
+				anchorPoints: {
+					JBegin: entry.jAnchorPoints.jBegin,
+					FR4Begin: entry.jAnchorPoints.fr4Begin,
+					FR4End: entry.jAnchorPoints.fr4End
+				}
+			})
+			fragments = append(fragments, {
+				uri: jUri,
+				range: { from: 0, to: len(entry.jSequence) },
+				sequence: entry.jSequence
+			})
+		}
+		library := [{
+			taxonId: 1111,
+			speciesNames: ["custom"],
+			genes: genes,
+			sequenceFragments: fragments,
+			checksumVersion: 1
+		}]
+		referenceLibrary = string(json.encode(library))
+	} else if mode == "libraryFile" {
 		fImport := file.importFile(args.libraryFile)
     	libraryImportHandle = fImport.handle
     	referenceLibrary = fImport.file
 	} else {
+		// fastaSequence or fastaFile — both use vGenes/jGenes via repseqio
 		repseqioResults := render.create(repseqioLibraryTpl, {
 			vGenes: args.vGenes,
 			jGenes: args.jGenes,
@@ -101,7 +166,7 @@ wf.body(func(args) {
 		}
 	}
 
-	if !is_undefined(args.libraryFile) {
+	if mode == "libraryFile" {
 		exports.library = {
 			data: referenceLibrary,
 			spec: {
@@ -127,7 +192,9 @@ wf.body(func(args) {
 		progress: runMixcr.output("progress.data"),
 		clonotypeTables: pframes.exportFrame(runMixcr.output("clonotypeTables"))
 	}
-	outputs.referenceLibrary = file.exportFile(referenceLibrary)
+	if mode != "buildLibrary" {
+		outputs.referenceLibrary = file.exportFile(referenceLibrary)
+	}
 	if !is_undefined(debugOutput) {
 		outputs.debugOutput = debugOutput
 	}

package/src/mixcr-analyze.tpl.tengo

@@ -89,8 +89,15 @@ self.body(func(inputs) {
     mixcrCmdBuilder.
         arg("--assemble-clonotypes-by").arg(formatAssemblingFeature(params.assemblingFeature)).
         arg("--species").arg("custom").
-		arg("--library").arg(libraryFileName).
-		addFile(libraryFileName, params.referenceLibrary).
+		arg("--library").arg(libraryFileName)
+
+	if is_string(params.referenceLibrary) {
+		mixcrCmdBuilder.writeFile(libraryFileName, params.referenceLibrary).saveFile(libraryFileName)
+	} else {
+		mixcrCmdBuilder.addFile(libraryFileName, params.referenceLibrary)
+	}
+
+    mixcrCmdBuilder.
         arg("--rna").
 		arg("--force-overwrite").
 		arg("--rigid-left-alignment-boundary").

package/src/mixcr-export.tpl.tengo

@@ -221,12 +221,19 @@ self.body(func(inputs) {
 			libraryFileName = "library.json.gz"
 		}
 
-		return mixcrCmdBuilder.
+		mixcrCmdBuilder.
 			arg("clones.clns").
 			addFile("clones.clns", clnsFile).
 			arg("clones.tsv").
-			saveFile("clones.tsv").
-			addFile(libraryFileName, params.referenceLibrary).
+			saveFile("clones.tsv")
+
+		if is_string(params.referenceLibrary) {
+			mixcrCmdBuilder.writeFile(libraryFileName, params.referenceLibrary).saveFile(libraryFileName)
+		} else {
+			mixcrCmdBuilder.addFile(libraryFileName, params.referenceLibrary)
+		}
+
+		return mixcrCmdBuilder.
 			cacheHours(3).
 			run()
 	}

package/src/prerun.tpl.tengo

@@ -0,0 +1,34 @@
+wf := import("@platforma-sdk/workflow-tengo:workflow")
+render := import("@platforma-sdk/workflow-tengo:render")
+assets := import("@platforma-sdk/workflow-tengo:assets")
+file := import("@platforma-sdk/workflow-tengo:file")
+
+repseqioLibraryTpl := assets.importTemplate(":repseqio-library")
+
+wf.body(func(args) {
+	outputs := {}
+
+	if args.referenceInputMode == "buildLibrary" && !is_undefined(args.buildLibraryVGenes) && !is_undefined(args.buildLibraryJGenes) {
+		chainInfos := {
+			"IGHeavy": "IGH",
+			"IGLight": "IGK",
+			"TCRAlpha": "TRA",
+			"TCRBeta": "TRB",
+			"TCRGamma": "TRD",
+			"TCRDelta": "TRG"
+		}
+		chains := chainInfos[args.chains]
+
+		repseqioResults := render.createEphemeral(repseqioLibraryTpl, {
+			vGenes: args.buildLibraryVGenes,
+			jGenes: args.buildLibraryJGenes,
+			chains: chains
+		})
+		outputs.referenceLibrary = file.exportFile(repseqioResults.output("referenceLibrary"))
+	}
+
+	return {
+		outputs: outputs,
+		exports: {}
+	}
+})