@platforma-open/milaboratories.top-antibodies.workflow 1.4.0 → 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@1.4.0 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 +1,18 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.6.0
+
+### Minor Changes
+
+- d32234f: Support batch system
+
+## 1.5.0
+
+### Minor Changes
+
+- bf454d4: Default ranking column in case user does not select one
+- 4990fd8: Fix empty top and ranking cases
+
 ## 1.4.0
 
 ### Minor Changes

package/package.json

@@ -1,17 +1,17 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.4.0",
+  "version": "1.6.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.7.1",
+    "@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.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

@@ -16,10 +16,17 @@ wf.prepare(func(args){
 	bundleBuilder.ignoreMissingDomains() // to make query work for both bulk and single cell data
 	bundleBuilder.addAnchor("main", args.inputAnchor) 
 	
-	for col in args.rankingOrder {
-		bundleBuilder.addAnchor(col.value.anchorName, col.value.anchorRef)
-		bundleBuilder.addSingle(col.value.column)
+	if len(args.rankingOrder) > 0 {
+		for col in args.rankingOrder {
+			bundleBuilder.addAnchor(col.value.anchorName, col.value.anchorRef)
+			bundleBuilder.addSingle(col.value.column)
+		}
+	} else {
+		bundleBuilder.addAnchor(args.rankingOrderDefault.value.anchorName, 
+								args.rankingOrderDefault.value.anchorRef)
+		bundleBuilder.addSingle(args.rankingOrderDefault.value.column)
 	}
+	
 
 	// Add linker column
 	bundleBuilder.addMulti({
@@ -89,46 +96,68 @@ wf.body(func(args) {
 
 	////////// Clonotype Filtering //////////
 	
-	// Build clonotype table
-	cloneTable := pframes.csvFileBuilder() 
-	cloneTable.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
-	
-	for i, col in args.rankingOrder {
-		cloneTable.add(columns.getColumn(col.value.column), {header: "Col" + string(i)})
-	
-		// If column does not have main anchor axis we have to include theirs
-		colsSpec := columns.getSpec(col.value.column)
-		axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
-		if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
-			for na, ax in colsSpec.axesSpec {
-				if ax.name != datasetSpec.axesSpec[1].name {
-					cloneTable.setAxisHeader(ax.name, "cluster_" + string(i) + string(na))
-				}
-			}
-		}	
-	}
+	topClonotypesCsv := undefined
 
-	// Columns gotten by query require .key
-	linkerAxisSpec := {}
-	for i, col in columns.getColumns("linkers") {
-		if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
-			cloneTable.add(col, {header: "linker." + string(i)})
-			cloneTable.setAxisHeader(col.spec.axesSpec[0].name, "cluster_" + string(i))
-			linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[0]
-		} else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
-			cloneTable.add(col, {header: "linker." + string(i)})
-			cloneTable.setAxisHeader(col.spec.axesSpec[1].name, "cluster_" + string(i))
-			linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[1]
+	if topClonotypes != undefined {
+		// Build clonotype table
+		cloneTable := pframes.csvFileBuilder() 
+		cloneTable.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
+		
+		if len(args.rankingOrder) > 0 {
+			for i, col in args.rankingOrder {
+				cloneTable.add(columns.getColumn(col.value.column), {header: "Col" + string(i)})
+			
+				// If column does not have main anchor axis we have to include theirs
+				colsSpec := columns.getSpec(col.value.column)
+				axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
+				if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
+					for na, ax in colsSpec.axesSpec {
+						if ax.name != datasetSpec.axesSpec[1].name {
+							cloneTable.setAxisHeader(ax.name, "cluster_" + string(i) + string(na))
+						}
+					}
+				}	
+			}
+		} else {
+			i := 0
+			cloneTable.add(columns.getColumn(args.rankingOrderDefault.value.column), {header: "Col" + string(i)})
+		
+			// If column does not have main anchor axis we have to include theirs
+			colsSpec := columns.getSpec(args.rankingOrderDefault.value.column)
+			axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
+			if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
+				for na, ax in colsSpec.axesSpec {
+					if ax.name != datasetSpec.axesSpec[1].name {
+						cloneTable.setAxisHeader(ax.name, "cluster_" + string(i) + string(na))
+					}
+				}
+			}	
 		}
-	}
-	cloneTable = cloneTable.build()
 
-	topClonotypesCsv := undefined
+		// Columns gotten by query require .key
+		linkerAxisSpec := {}
+		if len(columns.getColumns("linkers")) > 0 {
+			for i, col in columns.getColumns("linkers") {
+				if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
+					cloneTable.add(col, {header: "linker." + string(i)})
+					cloneTable.setAxisHeader(col.spec.axesSpec[0].name, "cluster_" + string(i))
+					linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[0]
+				} else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
+					cloneTable.add(col, {header: "linker." + string(i)})
+					cloneTable.setAxisHeader(col.spec.axesSpec[1].name, "cluster_" + string(i))
+					linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[1]
+				}
+			}
+		}
+		cloneTable.mem("16GiB")
+		cloneTable.cpu(1)
+		cloneTable = cloneTable.build()
 
-	if topClonotypes != undefined {
 		// 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)).
@@ -144,7 +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)
 	}
 
@@ -203,11 +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").
@@ -231,11 +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 {