@platforma-open/milaboratories.top-antibodies.workflow 1.14.0 → 1.15.0

package/.turbo/turbo-build.log

@@ -1,24 +1,24 @@
  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@1.14.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@1.15.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/assembling-fasta.tpl.tengo"...
-Processing "src/libs/data-utils.lib.tengo"...
-Processing "src/libs/pf-kabat-conv.lib.tengo"...
-Processing "src/libs/pf-spectratype-conv.lib.tengo"...
-Processing "src/libs/pf-vj-usage-conv.lib.tengo"...
-Processing "src/libs/sampled-cols-conv.lib.tengo"...
+Processing "src/filter-and-sample.tpl.tengo"...
 Processing "src/main.tpl.tengo"...
+Processing "src/pf-kabat-conv.lib.tengo"...
+Processing "src/pf-spectratype-conv.lib.tengo"...
+Processing "src/pf-vj-usage-conv.lib.tengo"...
 Processing "src/prerun.tpl.tengo"...
+Processing "src/sampled-cols-conv.lib.tengo"...
 No syntax errors found.
   info: Compiling 'dist'...
-  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/libs.data-utils.lib.tengo
-  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/libs.pf-kabat-conv.lib.tengo
-  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/libs.pf-spectratype-conv.lib.tengo
-  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/libs.pf-vj-usage-conv.lib.tengo
-  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/libs.sampled-cols-conv.lib.tengo
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/pf-kabat-conv.lib.tengo
+  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/assembling-fasta.plj.gz
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/tpl/filter-and-sample.plj.gz
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/tpl/prerun.plj.gz
   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.

package/CHANGELOG.md

@@ -1,5 +1,23 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.15.0
+
+### Minor Changes
+
+- 00143a9: multiple clustering blocks fix, columns names fix, dependencies updates
+
+## 1.14.1
+
+### Patch Changes
+
+- b99b7ba: Revert optimization changes
+- Updated dependencies [b99b7ba]
+  - @platforma-open/milaboratories.top-antibodies.sample-clonotypes@1.7.1
+  - @platforma-open/milaboratories.top-antibodies.assembling-fasta@1.2.1
+  - @platforma-open/milaboratories.top-antibodies.anarci-kabat@1.2.1
+  - @platforma-open/milaboratories.top-antibodies.spectratype@1.7.1
+  - @platforma-open/milaboratories.top-antibodies.umap@1.2.1
+
 ## 1.14.0
 
 ### Minor Changes

package/dist/index.cjs

@@ -1,5 +1,6 @@
 module.exports = { Templates: {
   'assembling-fasta': { type: 'from-file', path: require.resolve('./tengo/tpl/assembling-fasta.plj.gz') },
+  'filter-and-sample': { type: 'from-file', path: require.resolve('./tengo/tpl/filter-and-sample.plj.gz') },
   'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
 }};

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "assembling-fasta" | "prerun" | "main";
+declare type TplName = "assembling-fasta" | "filter-and-sample" | "prerun" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -1,6 +1,7 @@
 import { resolve } from 'node:path';
 export const Templates = {
   'assembling-fasta': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/assembling-fasta.plj.gz') },
+  'filter-and-sample': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/filter-and-sample.plj.gz') },
   'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
 };

package/dist/tengo/lib/{libs.pf-kabat-conv.lib.tengo → pf-kabat-conv.lib.tengo}

@@ -19,7 +19,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
         annotations: {
           "pl7.app/label": "KABAT sequence " + featureName + " Heavy",
           "pl7.app/table/orderPriority": "10",
-	      "pl7.app/table/visibility": "default"
+		      "pl7.app/table/visibility": "default"
         }
       }
     },
@@ -34,7 +34,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
         annotations: {
           "pl7.app/label": "KABAT positions " + featureName + " Heavy",
           "pl7.app/table/orderPriority": "9",
-	      "pl7.app/table/visibility": "optional"
+		      "pl7.app/table/visibility": "optional"
         }
       }
     }
@@ -53,7 +53,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
           annotations: {
             "pl7.app/label": "KABAT sequence " + featureName + " Light",
             "pl7.app/table/orderPriority": "8",
-	        "pl7.app/table/visibility": "default"
+		        "pl7.app/table/visibility": "default"
           }
         }
       },
@@ -68,7 +68,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
           annotations: {
             "pl7.app/label": "KABAT positions " + featureName + " Light",
             "pl7.app/table/orderPriority": "7",
-	        "pl7.app/table/visibility": "optional"
+		        "pl7.app/table/visibility": "optional"
           }
         }
       }
@@ -128,3 +128,4 @@ export ll.toStrict({
   getColumns: getColumns
 })
 
+

package/{src/libs → dist/tengo/lib}/pf-spectratype-conv.lib.tengo

@@ -57,4 +57,3 @@ getColumns := func() {
 export ll.toStrict({
     getColumns: getColumns
 })
-

package/{src/libs → dist/tengo/lib}/pf-vj-usage-conv.lib.tengo

@@ -52,4 +52,3 @@ getColumns := func() {
 export ll.toStrict({
     getColumns: getColumns
 })
-

package/{src/libs → dist/tengo/lib}/sampled-cols-conv.lib.tengo

@@ -48,4 +48,3 @@ getColumns := func(datasetSpec, addRanking) {
 export ll.toStrict({
 	getColumns: getColumns
 })
-

package/package.json

@@ -1,20 +1,20 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.14.0",
+  "version": "1.15.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.6.4",
+    "@platforma-sdk/workflow-tengo": "^5.6.6",
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
-    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.7.0",
-    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.0",
-    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.2.0",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.7.0",
-    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.2.0"
+    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.7.1",
+    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.1",
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.7.1",
+    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.2.1",
+    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.2.1"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.3.14",
-    "@platforma-sdk/test": "^1.46.3",
+    "@platforma-sdk/tengo-builder": "^2.4.0",
+    "@platforma-sdk/test": "^1.47.3",
     "vitest": "^2.1.8"
   },
   "scripts": {

package/src/assembling-fasta.tpl.tengo

@@ -12,7 +12,7 @@ self.body(func(inputs) {
 
     inputTsv := inputs.inputTsv
     keyColumn := inputs.keyColumn // "clonotypeKey" or "scClonotypeKey"
-    finalClonotypesParquet := inputs.finalClonotypesParquet // optional
+    finalClonotypesCsv := inputs.finalClonotypesCsv // optional
     isSingleCell := inputs.isSingleCell // boolean
     bulkChain := inputs.bulkChain // "H" or "KL" when !isSingleCell
 
@@ -25,9 +25,9 @@ self.body(func(inputs) {
         arg("--key_column").arg(keyColumn).
         arg("--output_fasta").arg("assembling.fasta")
 
-    if finalClonotypesParquet != undefined {
-        cmd = cmd.addFile("finalClonotypes.parquet", finalClonotypesParquet).
-            arg("--final_clonotypes_parquet").arg("finalClonotypes.parquet")
+    if finalClonotypesCsv != undefined {
+        cmd = cmd.addFile("finalClonotypes.csv", finalClonotypesCsv).
+            arg("--final_clonotypes_csv").arg("finalClonotypes.csv")
     }
 
     cmd = cmd.saveFile("assembling.fasta").

package/src/filter-and-sample.tpl.tengo

@@ -0,0 +1,81 @@
+// Template for clonotype filtering and sampling
+self := import("@platforma-sdk/workflow-tengo:tpl")
+exec := import("@platforma-sdk/workflow-tengo:exec")
+assets := import("@platforma-sdk/workflow-tengo:assets")
+pframes := import("@platforma-sdk/workflow-tengo:pframes")
+xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
+render := import("@platforma-sdk/workflow-tengo:render")
+sampledColsConv := import(":sampled-cols-conv")
+json := import("json")
+
+self.defineOutputs("sampledRows", "finalClonotypesCsv")
+
+self.body(func(inputs) {
+
+    cloneTable := inputs.cloneTable
+    datasetSpec := inputs.datasetSpec
+    filterMap := inputs.filterMap
+    rankingMap := inputs.rankingMap
+    topClonotypes := inputs.topClonotypes
+
+    outputs := {}
+    finalClonotypesCsv := undefined
+    
+    // Run filtering script
+    filterResult := exec.builder().
+        software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.sample-clonotypes:filter")).
+        mem("16GiB").
+        cpu(1).
+        addFile("clonotypes.csv", cloneTable).
+        arg("--csv").arg("clonotypes.csv").
+        arg("--out").arg("filteredClonotypes.csv").
+        arg("--filter-map").arg(string(json.encode(filterMap))).
+        saveFile("filteredClonotypes.csv").
+        printErrStreamToStdout().
+        cache(24 * 60 * 60 * 1000).
+        run()
+
+    // Save filtered CSV file
+    filteredClonotypesCsv := filterResult.getFile("filteredClonotypes.csv")
+
+    // Store outputs 
+    sampledColsParams := sampledColsConv.getColumns(datasetSpec, false) // No ranking column
+    filteredClonotypesPf := xsv.importFile(filteredClonotypesCsv, "csv", sampledColsParams,
+                                        {cpu: 1, mem: "16GiB"})
+
+    // Prepare outputs in case there is no top ranking
+    outputs["sampledRows"] = pframes.exportFrame(filteredClonotypesPf)
+    finalClonotypesCsv = filteredClonotypesCsv
+
+	if topClonotypes != undefined {
+
+		////////// Top Clonotypes Sampling //////////
+		// Run sampling script on filtered data
+		sampleClones := exec.builder().
+			software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.sample-clonotypes:main")).
+			mem("16GiB").
+			cpu(1).
+			addFile("filteredClonotypes.csv", filteredClonotypesCsv).
+			arg("--csv").arg("filteredClonotypes.csv").
+			arg("--n").arg(string(topClonotypes)).
+			arg("--ranking-map").arg(string(json.encode(rankingMap))).
+			arg("--out").arg("sampledClonotypes_top.csv").
+			saveFile("sampledClonotypes_top.csv").
+			printErrStreamToStdout().
+			cache(24 * 60 * 60 * 1000).
+			run()
+
+		// Save top clonotypes CSV file
+		finalClonotypesCsv = sampleClones.getFile("sampledClonotypes_top.csv")
+		
+		// Store outputs 
+        sampledColsParams := sampledColsConv.getColumns(datasetSpec, true) // Add ranking column
+		sampledColumnsPf := xsv.importFile(finalClonotypesCsv, "csv", sampledColsParams,
+											{cpu: 1, mem: "16GiB"})
+		outputs["sampledRows"] = pframes.exportFrame(sampledColumnsPf)
+	} 
+
+    outputs["finalClonotypesCsv"] = finalClonotypesCsv
+
+    return outputs
+}) 

package/src/{libs/pf-kabat-conv.lib.tengo → pf-kabat-conv.lib.tengo}

@@ -19,7 +19,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
         annotations: {
           "pl7.app/label": "KABAT sequence " + featureName + " Heavy",
           "pl7.app/table/orderPriority": "10",
-	      "pl7.app/table/visibility": "default"
+		      "pl7.app/table/visibility": "default"
         }
       }
     },
@@ -34,7 +34,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
         annotations: {
           "pl7.app/label": "KABAT positions " + featureName + " Heavy",
           "pl7.app/table/orderPriority": "9",
-	      "pl7.app/table/visibility": "optional"
+		      "pl7.app/table/visibility": "optional"
         }
       }
     }
@@ -53,7 +53,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
           annotations: {
             "pl7.app/label": "KABAT sequence " + featureName + " Light",
             "pl7.app/table/orderPriority": "8",
-	        "pl7.app/table/visibility": "default"
+		        "pl7.app/table/visibility": "default"
           }
         }
       },
@@ -68,7 +68,7 @@ getColumns := func(datasetSpec, featureName, bulkChain) {
           annotations: {
             "pl7.app/label": "KABAT positions " + featureName + " Light",
             "pl7.app/table/orderPriority": "7",
-	        "pl7.app/table/visibility": "optional"
+		        "pl7.app/table/visibility": "optional"
           }
         }
       }
@@ -128,3 +128,4 @@ export ll.toStrict({
   getColumns: getColumns
 })
 
+

package/{dist/tengo/lib/libs.pf-spectratype-conv.lib.tengo → src/pf-spectratype-conv.lib.tengo}

@@ -57,4 +57,3 @@ getColumns := func() {
 export ll.toStrict({
     getColumns: getColumns
 })
-

package/{dist/tengo/lib/libs.pf-vj-usage-conv.lib.tengo → src/pf-vj-usage-conv.lib.tengo}

@@ -52,4 +52,3 @@ getColumns := func() {
 export ll.toStrict({
     getColumns: getColumns
 })
-