@platforma-open/milaboratories.immune-assay-data.workflow 1.8.1 → 1.10.0

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@1.8.1 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
+> @platforma-open/milaboratories.immune-assay-data.workflow@1.10.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/analysis.tpl.tengo"...
@@ -9,6 +9,7 @@ Processing "src/check-content-empty.tpl.tengo"...
 Processing "src/extract-unique-values.tpl.tengo"...
 Processing "src/get-unique-values.tpl.tengo"...
 Processing "src/main.tpl.tengo"...
+Processing "src/prerun.tpl.tengo"...
 Processing "src/process-outputs.tpl.tengo"...
 Processing "src/run-alignment.tpl.tengo"...
 No syntax errors found.
@@ -17,6 +18,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/check-content-empty.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/extract-unique-values.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/get-unique-values.plj.gz
+  info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/prerun.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/process-outputs.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/run-alignment.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/analysis.plj.gz

package/CHANGELOG.md

@@ -1,5 +1,21 @@
 # @platforma-open/milaboratories.immune-assay-data.workflow
 
+## 1.10.0
+
+### Minor Changes
+
+- 29a44a2: Improved performance on large datasets
+
+## 1.9.0
+
+### Minor Changes
+
+- 4a7083b: Fix assay file import to support remote (non-local) files
+
+  Previously, column detection used `lsDriver.getLocalFileContent()` which only works for locally-mounted files. Files from remote storages would silently fail, leaving the block unconfigurable.
+
+  Now uses a prerun workflow step to import the file and expose it as a blob, and `ReactiveFileContent` in the UI to read it via `blobDriver` — the same pattern used by samples-and-data. This works for both local and remote files.
+
 ## 1.8.1
 
 ### Patch Changes

package/dist/index.cjs

@@ -3,6 +3,7 @@ module.exports = { Templates: {
   'check-content-empty': { type: 'from-file', path: require.resolve('./tengo/tpl/check-content-empty.plj.gz') },
   'extract-unique-values': { type: 'from-file', path: require.resolve('./tengo/tpl/extract-unique-values.plj.gz') },
   'get-unique-values': { type: 'from-file', path: require.resolve('./tengo/tpl/get-unique-values.plj.gz') },
+  'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'process-outputs': { type: 'from-file', path: require.resolve('./tengo/tpl/process-outputs.plj.gz') },
   'run-alignment': { type: 'from-file', path: require.resolve('./tengo/tpl/run-alignment.plj.gz') },
   'analysis': { type: 'from-file', path: require.resolve('./tengo/tpl/analysis.plj.gz') },

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "build-outputs" | "check-content-empty" | "extract-unique-values" | "get-unique-values" | "process-outputs" | "run-alignment" | "analysis" | "main";
+declare type TplName = "build-outputs" | "check-content-empty" | "extract-unique-values" | "get-unique-values" | "prerun" | "process-outputs" | "run-alignment" | "analysis" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -4,6 +4,7 @@ export const Templates = {
   'check-content-empty': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/check-content-empty.plj.gz') },
   'extract-unique-values': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/extract-unique-values.plj.gz') },
   'get-unique-values': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/get-unique-values.plj.gz') },
+  'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'process-outputs': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process-outputs.plj.gz') },
   'run-alignment': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/run-alignment.plj.gz') },
   'analysis': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/analysis.plj.gz') },

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@platforma-open/milaboratories.immune-assay-data.workflow",
-  "version": "1.8.1",
+  "version": "1.10.0",
   "type": "module",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.9.1",
+    "@platforma-sdk/workflow-tengo": "5.11.0",
     "@platforma-open/soedinglab.software-mmseqs2": "1.18.3",
     "@platforma-open/milaboratories.immune-assay-data.prepare-fasta": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.add-header": "1.1.3",
@@ -14,7 +14,7 @@
     "@platforma-open/milaboratories.immune-assay-data.check-content-empty": "1.0.1"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.28"
+    "@platforma-sdk/tengo-builder": "2.5.5"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/main.tpl.tengo

@@ -11,10 +11,13 @@ text := import("text")
 render := import("@platforma-sdk/workflow-tengo:render")
 strings := import("@platforma-sdk/workflow-tengo:strings")
 
+prerunTpl := assets.importTemplate(":prerun")
 analysisTpl := assets.importTemplate(":analysis")
 processOutputsTpl := assets.importTemplate(":process-outputs")
 checkContentEmptyTpl := assets.importTemplate(":check-content-empty")
 
+wf.setPreRun(prerunTpl)
+
 prepareFastaSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.prepare-fasta:main")
 checkContentEmptySw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.check-content-empty:main")
 

package/src/prerun.tpl.tengo

@@ -0,0 +1,17 @@
+wf := import("@platforma-sdk/workflow-tengo:workflow")
+file := import("@platforma-sdk/workflow-tengo:file")
+
+wf.body(func(args) {
+	if is_undefined(args.fileHandle) {
+		return { outputs: {}, exports: {} }
+	}
+
+	importedFile := file.importFile(args.fileHandle)
+
+	return {
+		outputs: {
+			assayFile: file.exportFile(importedFile.file)
+		},
+		exports: {}
+	}
+})

package/src/run-alignment.tpl.tengo

@@ -2,6 +2,7 @@ self := import("@platforma-sdk/workflow-tengo:tpl")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 exec := import("@platforma-sdk/workflow-tengo:exec")
 assets:= import("@platforma-sdk/workflow-tengo:assets")
+math := import("math")
 mmseqsSw := assets.importSoftware("@platforma-open/soedinglab.software-mmseqs2:main")
 
 self.defineOutputs("mmseqsOutput")
@@ -16,15 +17,20 @@ self.body(func(args) {
     clonesFasta := args.clonesFasta
     assayFasta := args.assayFasta
 
-	mem := "8GiB"
-	cpu := 1
+	baseMemGiB := 64
 	if !is_undefined(args.metaInputs.mem) {
-		mem = string(args.metaInputs.mem) + "GiB"
+		baseMemGiB = args.metaInputs.mem
 	}
+	mem := string(int(math.max(64, baseMemGiB))) + "GiB"
+	cpu := 1
 	if !is_undefined(args.metaInputs.cpu) {
 		cpu = args.metaInputs.cpu
 	}
 
+	// Cap mmseqs2 in-RAM usage to 80% of allocated memory so it splits to disk
+	// rather than getting OOM-killed by the kernel on large datasets.
+	memLimit := "{int(ceil(system.ram.gb * 0.8))}" + "G"
+
 	mmseqs := exec.builder().
 		software(mmseqsSw).
 		mem(mem).
@@ -34,6 +40,7 @@ self.body(func(args) {
 		arg("clones.fasta").
 		arg("results.tsv").
 		arg("tmp").
+		arg("--split-memory-limit").argWithVar(memLimit).
 		arg("--threads").arg(string(cpu)).
 		arg("--max-seqs").arg("10000").
 		arg("--search-type").arg(mmseqsSearchType).