@platforma-open/milaboratories.top-antibodies.workflow 1.5.0 → 1.6.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
- WARN  Issue while reading "/home/runner/work/top-antibodies/top-antibodies/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+ WARN  Issue while reading "/home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.top-antibodies.workflow@1.5.0 build /home/runner/work/top-antibodies/top-antibodies/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@1.6.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/main.tpl.tengo"...
@@ -9,9 +9,9 @@ Processing "src/pf-vj-usage-conv.lib.tengo"...
 Processing "src/sampled-cols-conv.lib.tengo"...
 No syntax errors found.
   info: Compiling 'dist'...
-  info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/pf-spectratype-conv.lib.tengo
-  info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/pf-vj-usage-conv.lib.tengo
-  info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/sampled-cols-conv.lib.tengo
-  info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/tpl/main.plj.gz
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/pf-spectratype-conv.lib.tengo
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/pf-vj-usage-conv.lib.tengo
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/sampled-cols-conv.lib.tengo
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/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.top-antibodies.workflow
 
+## 1.6.0
+
+### Minor Changes
+
+- d32234f: Support batch system
+
 ## 1.5.0
 
 ### Minor Changes

package/package.json

@@ -1,17 +1,17 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.5.0",
+  "version": "1.6.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.7.1",
-    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.0.3",
+    "@platforma-sdk/workflow-tengo": "^4.7.4",
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.3.2",
     "@platforma-open/milaboratories.top-antibodies.umap": "1.0.3",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.3.2"
+    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.0.3"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.1.7",
-    "@platforma-sdk/test": "^1.33.10",
+    "@platforma-sdk/tengo-builder": "^2.1.10",
+    "@platforma-sdk/test": "1.32.11",
     "vitest": "^2.1.8"
   },
   "scripts": {

package/src/main.tpl.tengo

@@ -149,11 +149,15 @@ wf.body(func(args) {
 				}
 			}
 		}
+		cloneTable.mem("16GiB")
+		cloneTable.cpu(1)
 		cloneTable = cloneTable.build()
 
 		// Run sampling script
 		sampleClones := exec.builder().
 			software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.sample-clonotypes:main")).
+			mem("16GiB").
+			cpu(1).
 			addFile("filteredClonotypes.csv", cloneTable).
 			arg("--csv").arg("filteredClonotypes.csv").
 			arg("--n").arg(string(topClonotypes)).
@@ -169,7 +173,8 @@ wf.body(func(args) {
 
 		// Store outputs
 		sampledColsParams := sampledColsConv.getColumns(datasetSpec)
-		sampledColumnsPf := xsv.importFile(topClonotypesCsv, "csv", sampledColsParams)
+		sampledColumnsPf := xsv.importFile(topClonotypesCsv, "csv", sampledColsParams,
+											{cpu: 1, mem: "16GiB"})
 		outputs["sampledRows"] = pframes.exportFrame(sampledColumnsPf)
 	}
 
@@ -228,11 +233,14 @@ wf.body(func(args) {
 		headerName := makeHeaderName(col, "jGene", isSingleCell)
 		cdr3SeqTable.add(col, {header: headerName})
 	}
-
+	cdr3SeqTable.mem("16GiB")
+	cdr3SeqTable.cpu(1)
 	cdr3SeqTableBuilt := cdr3SeqTable.build()
 
 	cdr3VspectratypeCmd := exec.builder().
 		software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.spectratype:main")).
+		mem("16GiB").
+		cpu(1).
 		addFile("cdr3_sequences_input.tsv", cdr3SeqTableBuilt).
 		arg("--input_tsv").arg("cdr3_sequences_input.tsv").
 		arg("--spectratype_tsv").arg("spectratype.tsv").
@@ -256,11 +264,15 @@ wf.body(func(args) {
 
 	// For spectratype structure is [chain][cdr3Length][vGene] -> count
 
-	cdr3VspectratypePf := xsv.importFile(cdr3VspectratypeCmd.getFile("spectratype.tsv"), "tsv", spectratypeConv.getColumns())
+	cdr3VspectratypePf := xsv.importFile(cdr3VspectratypeCmd.getFile("spectratype.tsv"), 
+										"tsv", spectratypeConv.getColumns(),
+										{cpu: 1, mem: "16GiB"})
 	outputs["cdr3VspectratypePf"] = pframes.exportFrame(cdr3VspectratypePf) 
 
 	// For vjUsage structure is [chain][vGene][jGene] -> count
-	vjUsagePf := xsv.importFile(cdr3VspectratypeCmd.getFile("vj_usage.tsv"), "tsv", vjUsageConv.getColumns())
+	vjUsagePf := xsv.importFile(cdr3VspectratypeCmd.getFile("vj_usage.tsv"), 
+								"tsv", vjUsageConv.getColumns(), 
+								{cpu: 1, mem: "16GiB"})
 	outputs["vjUsagePf"] = pframes.exportFrame(vjUsagePf)
 
 	return {