@platforma-open/milaboratories.immune-assay-data.workflow 1.1.0 → 1.2.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/immune-assay-data/immune-assay-data/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.immune-assay-data.workflow@1.1.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
+> @platforma-open/milaboratories.immune-assay-data.workflow@1.2.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/main.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.immune-assay-data.workflow
 
+## 1.2.0
+
+### Minor Changes
+
+- bd219bf: Update SDK and bugfixes
+
 ## 1.1.0
 
 ### Minor Changes

package/package.json

@@ -1,18 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.immune-assay-data.workflow",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.7.1",
+    "@platforma-sdk/workflow-tengo": "^4.9.0",
     "@platforma-open/soedinglab.software-mmseqs2": "^1.0.0",
     "@platforma-open/milaboratories.immune-assay-data.prepare-fasta": "1.0.3",
     "@platforma-open/milaboratories.immune-assay-data.add-header": "1.0.2",
     "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.0.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.1.7",
-    "@platforma-sdk/test": "^1.31.16",
+    "@platforma-sdk/tengo-builder": "^2.1.11",
+    "@platforma-sdk/test": "^1.37.8",
     "vitest": "^2.1.8"
   },
   "scripts": {

package/src/main.tpl.tengo

@@ -7,17 +7,15 @@ maps:= import("@platforma-sdk/workflow-tengo:maps")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
 pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
-slices := import("@platforma-sdk/workflow-tengo:slices")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 path := import("@platforma-sdk/workflow-tengo:path")
 json := import("json")
-strings := import("@platforma-sdk/workflow-tengo:strings")
 text := import("text")
 render := import("@platforma-sdk/workflow-tengo:render")
+strings := import("@platforma-sdk/workflow-tengo:strings")
 runAlignmentTpl := assets.importTemplate(":run-alignment")
 
 prepareFastaSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.prepare-fasta:main")
-mmseqsSw := assets.importSoftware("@platforma-open/soedinglab.software-mmseqs2:main")
 addHeaderSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.add-header:main")
 covModeCalcSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc:main")
 
@@ -81,6 +79,8 @@ prepareClonesTsv := func(args) {
 	cloneTable.setAxisHeader(datasetSpec.axesSpec[1].name, "seqId")
 	cloneTable.add(columns.getColumn(args.targetRef), {header: "sequence"})
 
+	cloneTable.mem("16GiB")
+	cloneTable.cpu(1)
 	return cloneTable.build()
 }
 
@@ -92,6 +92,8 @@ prepareClonesTsv := func(args) {
 runTsvToFasta := func(fileTsv) {
 	e := exec.builder().
 		software(prepareFastaSw).
+		mem("16GiB").
+		cpu(1).
 		addFile("input.tsv", fileTsv).
 		arg("-i").arg("input.tsv").
 		arg("-o").arg("output.fasta").
@@ -102,6 +104,10 @@ runTsvToFasta := func(fileTsv) {
 	return e.run()
 }
 
+assayColumnName := func(header) {
+	return "pl7.app/vdj/assay-data/" + strings.substituteSpecialCharacters(header)
+}
+
 wf.body(func(args) {
 	importFile := file.importFile(args.fileHandle)
 	datasetSpec := args.columns.getSpec(args.datasetRef)
@@ -159,6 +165,8 @@ wf.body(func(args) {
 	// Dynamically determine coverage mode by comparing average sequence lengths
 	coverageMode := exec.builder().
 		software(covModeCalcSw).
+		mem("16GiB").
+		cpu(1).
 		addFile("clones.fasta", clonesFasta).
 		addFile("assay.fasta", assayFasta).
 		arg("--clones-fasta").arg("clones.fasta").
@@ -199,6 +207,8 @@ wf.body(func(args) {
 	// @TODO remove header stuff and replace with pt when available (!)
 	addHeaderRunResult := exec.builder().
 		software(addHeaderSw).
+		mem("16GiB").
+		cpu(1).
 		arg("-i").arg("results.tsv").
 		arg("-o").arg("results_with_header.tsv").
 		addFile("results.tsv", mmseqsOutput).
@@ -300,6 +310,7 @@ wf.body(func(args) {
 			},	
 			{
 				column: sequenceColumnInfo.header,
+				id: strings.substituteSpecialCharacters(sequenceColumnInfo.header),
 				spec: {
 					name: "pl7.app/vdj/sequence",
 					valueType: "String",
@@ -338,8 +349,9 @@ wf.body(func(args) {
 			}
 			assayColumns = append(assayColumns, {
 				column: h.header,
+				id: strings.substituteSpecialCharacters(h.header),
 				spec: {
-					name: h.header,
+					name: assayColumnName(h.header),
 					valueType: h.type,
 					annotations: {	
 						"pl7.app/label": h.header,
@@ -368,7 +380,7 @@ wf.body(func(args) {
 			annotations: {
 				"pl7.app/isAnchor": "true"
 			}
-		})
+		}, {cpu: 1, mem: "16GiB"})
 
 		// "bits", "evalue", "pident"
 		cloneColumns := [
@@ -421,8 +433,9 @@ wf.body(func(args) {
 		for h in columnsToImport {
 			cloneColumns = append(cloneColumns, {
 				column: h.header,
+				id: strings.substituteSpecialCharacters(h.header),
 				spec: {
-					name: h.header,
+					name: assayColumnName(h.header),
 					valueType: h.type,
 					annotations: {	
 						"pl7.app/label": h.header,
@@ -447,7 +460,7 @@ wf.body(func(args) {
 				}],
 				columns: cloneColumns
 			},
-			{ splitDataAndSpec: true }
+			{ splitDataAndSpec: true, cpu: 1, mem: "16GiB" }
 		)
 
 		trace := pSpec.makeTrace(datasetSpec,

package/src/run-alignment.tpl.tengo

@@ -18,6 +18,8 @@ self.body(func(args) {
 
 	mmseqs := exec.builder().
 		software(mmseqsSw).
+		mem("32GiB").
+		cpu(1).
 		dontSaveStdoutOrStderr(). // important to avoid CID conflict problems coming from different stdout output on same datasets
 		arg("easy-search").
 		arg("clones.fasta").