@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.15.0 → 1.16.0

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@1.15.0 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
+> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.16.0 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"...

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow
 
+## 1.16.0
+
+### Minor Changes
+
+- 187f583: Fix repseqio fasta generation, dependencies updates
+
 ## 1.15.0
 
 ### Minor Changes

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow",
-  "version": "1.15.0",
+  "version": "1.16.0",
   "description": "MiXCR Amplicon Alignment Workflow",
   "type": "module",
   "dependencies": {
@@ -9,8 +9,8 @@
     "@platforma-open/milaboratories.software-repseqio": "^2.5.0-13-master"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.4.8",
-    "@platforma-sdk/test": "^1.51.6",
+    "@platforma-sdk/tengo-builder": "^2.4.11",
+    "@platforma-sdk/test": "^1.52.4",
     "vitest": "^4.0.17"
   },
   "scripts": {

package/src/main.tpl.tengo

@@ -32,27 +32,6 @@ wf.body(func(args) {
 	perProcessCPUs := args.perProcessCPUs
 	cloneClusteringMode := args.cloneClusteringMode
 
-	// Create V and J gene FASTA files
-	
-	fastaFileCmdBuilder := exec.builder().cmd("/usr/bin/env").arg("bash")
-	
-	// Save vGene to FASTA file if available
-	if args.vGenes != "" {
-		fastaFileCmdBuilder.writeFile("vGene.fasta", args.vGenes).
-            saveFile("vGene.fasta")
-	}
-	
-	// Save jGene to FASTA file if available
-	if args.jGenes != "" {
-		fastaFileCmdBuilder.writeFile("jGene.fasta", args.jGenes).
-            saveFile("jGene.fasta")
-	}
-
-    fastaFileCmd := fastaFileCmdBuilder.run()
-
-    vGeneFasta := fastaFileCmd.getFile("vGene.fasta")
-    jGeneFasta := fastaFileCmd.getFile("jGene.fasta")
-
 	chainInfos := {
 		"IGHeavy": { mixcrFilter: "IGH", name: "IG Heavy", shortName: "Heavy" },
 		"IGLight": { mixcrFilter: "IGK", name: "IG Light", shortName: "Light" },
@@ -65,8 +44,8 @@ wf.body(func(args) {
     // Generate reference library using repseqio if both V and J genes are available
   
 	repseqioResults := render.create(repseqioLibraryTpl, {
-		vGeneFasta: vGeneFasta,
-		jGeneFasta: jGeneFasta,
+		vGenes: args.vGenes,
+		jGenes: args.jGenes,
 		chains: chainInfos[chains].mixcrFilter
 	})
 	

package/src/repseqio-library.tpl.tengo

@@ -12,9 +12,6 @@ repseqioSw := assets.importSoftware("@platforma-open/milaboratories.software-rep
 self.defineOutputs("referenceLibrary", "debugOutput")
 
 self.body(func(inputs) {
-	// Get V and J gene FASTA files from prerun
-	vGeneFasta := inputs.vGeneFasta
-	jGeneFasta := inputs.jGeneFasta
 	
 	// Create repseqio command to generate reference library
 	repseqioVgeneCmd := exec.builder().
@@ -26,7 +23,8 @@ self.body(func(inputs) {
 		arg("--taxon-id").arg("1111").
 		arg("--gene-feature").arg("VRegion").
 		arg("--name-index").arg("0").
-		arg("vGene.fasta").addFile("vGene.fasta", vGeneFasta).
+		writeFile("vGene.fasta", inputs.vGenes).saveFile("vGene.fasta").
+		arg("vGene.fasta").
 		arg("vGene.json").saveFile("vGene.json").
 		cpu(1).mem("4GB")
 	
@@ -35,6 +33,7 @@ self.body(func(inputs) {
 	
 	// Get the generated reference library file
 	referenceLibraryVgene := repseqioVgeneResult.getFile("vGene.json")
+	vGeneFasta := repseqioVgeneResult.getFile("vGene.fasta")
 
 	repseqioJgeneCmd := exec.builder().
 		software(repseqioSw).
@@ -45,13 +44,14 @@ self.body(func(inputs) {
 		arg("--taxon-id").arg("1111").
 		arg("--gene-feature").arg("JRegion").
 		arg("--name-index").arg("0").
-		arg("jGene.fasta").addFile("jGene.fasta", jGeneFasta).
+		writeFile("jGene.fasta", inputs.jGenes).saveFile("jGene.fasta").
+		arg("jGene.fasta").
 		arg("jGene.json").saveFile("jGene.json").
 		cpu(1).mem("4GB")
 	
 	repseqioJgeneResult := repseqioJgeneCmd.run()
 	referenceLibraryJgene := repseqioJgeneResult.getFile("jGene.json")
-
+	jGeneFasta := repseqioJgeneResult.getFile("jGene.fasta")
 	repseqioMergeCmd := exec.builder().
 		software(repseqioSw).
 		arg("merge").