@platforma-open/milaboratories.mixcr-shm-trees.workflow 2.0.0 → 2.1.0

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 2.1.0
+
+### Minor Changes
+
+- 9c2dea0: SC trees
+
+## 2.0.1
+
+### Patch Changes
+
+- 589caf6: SDK upgrade
+
 ## 2.0.0
 
 ### Major Changes

package/dist/tengo/lib/export-settings.lib.tengo

@@ -13,9 +13,7 @@ text := import("text")
 allowNA := true
 
 // export of threes whithout nodes
-shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
-
+shmTreeTableOptions := func(dataDescription) {
     axes := []
     columns := []
     cmdArgs := []
@@ -33,7 +31,7 @@ shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -224,9 +222,7 @@ shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
 }
 
 // export data that is uniq for node
-shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
-
+shmTreeNodesTableOptions := func(dataDescription) {
     axes := []
     columns := []
     cmdArgs := []
@@ -244,7 +240,7 @@ shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -424,8 +420,7 @@ shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
 
 // export data that is unique for clones, but not unique for a node
 // (different clones could be in the same topology node, for example, different time points)
-shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
+shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     donorColumnSpec := donorColumn.get("spec").getDataAsJson()
 
     axes := []
@@ -445,7 +440,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -476,6 +471,8 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
     cmdArgs = append(cmdArgs, "-fileName")
     axes = append(axes, {
         "column": "fileName",
+        // in case of single cell trees, not all subtrees will be filled for nodes with observed
+        "allowNA": true,
         "preProcess": [
             {
                 "type": "regexpReplace",
@@ -490,6 +487,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
     axes = append(axes, {
         "column": "cloneId",
         "id": "clone-id",
+        "allowNA": true,
         "spec": {
             "name": "pl7.app/vdj/cloneId",
             "type": "Long",

package/package.json

@@ -1,19 +1,19 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "type": "module",
   "description": "Tengo-based template",
   "//": {
     "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^1.15.0",
-    "@platforma-sdk/workflow-tengo": "^1.6.3",
-    "@milaboratories/software-pframes-conv": "^1.6.3",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.14.4",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-113-develop",
-    "@platforma-sdk/test": "^1.7.16",
-    "vitest": "^2.1.3",
+    "@platforma-sdk/tengo-builder": "^1.16.1",
+    "@platforma-sdk/workflow-tengo": "^1.7.5",
+    "@milaboratories/software-pframes-conv": "^1.6.8",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.14.5",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-133-develop",
+    "@platforma-sdk/test": "^1.7.52",
+    "vitest": "^2.1.4",
     "typescript": "~5.5.4"
   },
   "scripts": {

package/src/export-settings.lib.tengo

@@ -13,9 +13,7 @@ text := import("text")
 allowNA := true
 
 // export of threes whithout nodes
-shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
-
+shmTreeTableOptions := func(dataDescription) {
     axes := []
     columns := []
     cmdArgs := []
@@ -33,7 +31,7 @@ shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -224,9 +222,7 @@ shmTreeTableOptions := func(dataDescription, runWithSingleCell) {
 }
 
 // export data that is uniq for node
-shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
-
+shmTreeNodesTableOptions := func(dataDescription) {
     axes := []
     columns := []
     cmdArgs := []
@@ -244,7 +240,7 @@ shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -424,8 +420,7 @@ shmTreeNodesTableOptions := func(dataDescription, runWithSingleCell) {
 
 // export data that is unique for clones, but not unique for a node
 // (different clones could be in the same topology node, for example, different time points)
-shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWithSingleCell) {
-    // TODO add forChain if runWithSingleCell
+shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     donorColumnSpec := donorColumn.get("spec").getDataAsJson()
 
     axes := []
@@ -445,7 +440,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
         }
     })
 
-    if runWithSingleCell && dataDescription["hasCellTags"] {
+    if dataDescription["cellsAssembled"] {
         cmdArgs = append(cmdArgs, "-subtreeId")
         axes = append(axes, {
             "column": "subtreeId",
@@ -476,6 +471,8 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
     cmdArgs = append(cmdArgs, "-fileName")
     axes = append(axes, {
         "column": "fileName",
+        // in case of single cell trees, not all subtrees will be filled for nodes with observed
+        "allowNA": true,
         "preProcess": [
             {
                 "type": "regexpReplace",
@@ -490,6 +487,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn, runWith
     axes = append(axes, {
         "column": "cloneId",
         "id": "clone-id",
+        "allowNA": true,
         "spec": {
             "name": "pl7.app/vdj/cloneId",
             "type": "Long",

package/src/process.tpl.tengo

@@ -25,7 +25,8 @@ self.body(func(inputs) {
 		"hasUmiTags": false,
 		"hasCellTags": false,
 		// will be filled
-		"coveredFeatures": []
+		"coveredFeatures": [],
+		"cellsAssembled": false
 	}
 
 	assemblingFeature := ""
@@ -38,6 +39,9 @@ self.body(func(inputs) {
 		if presetAnnotations["mixcr.com/umiTags"] != "" {
 			dataDescription["hasUmiTags"] = true
 		}
+		if presetAnnotations["mixcr.com/cellsAssembled"] == "true" {
+			dataDescription["cellsAssembled"] = true
+		}
 		dataDescription["coveredFeatures"] = text.re_split(',', presetAnnotations["mixcr.com/coveredFeaturesOnExport"])
 		// check that assemblingFeature feature is the same. If so, coveredFeatures will be the same too
 		if (assemblingFeature == "") {
@@ -51,9 +55,9 @@ self.body(func(inputs) {
 	dataGroupedByDonorId := prepareDonorColumn.groupDataByDonorId(inputs.donorColumn, inputs.datasets)
 
 	// collect params for running export commands and to parse result tsv files into pColumns
-	shmTreeTableOptions := exportSettings.shmTreeTableOptions(dataDescription, false)
-	shmTreeNodesTableOptions := exportSettings.shmTreeNodesTableOptions(dataDescription, false)
-	shmTreeNodesWithClonesTableOptions := exportSettings.shmTreeNodesWithClonesTableOptions(dataDescription, inputs.donorColumn, false)
+	shmTreeTableOptions := exportSettings.shmTreeTableOptions(dataDescription)
+	shmTreeNodesTableOptions := exportSettings.shmTreeNodesTableOptions(dataDescription)
+	shmTreeNodesWithClonesTableOptions := exportSettings.shmTreeNodesWithClonesTableOptions(dataDescription, inputs.donorColumn)
 
 	// TODO that call is too low level. Should be replaced with something that works with pColumns, not data only
 	mixcrResults := llPFrames.aggregate(

package/src/reconstruct-shm-trees.tpl.tengo

@@ -72,9 +72,7 @@ self.body(func(inputs) {
         arg("--report").arg("report.txt").
         saveFile("report.txt").
         arg("--json-report").arg("report.json").
-        saveFile("report.json").
-        // TODO support single cell trees
-        arg("--dont-combine-tree-by-cells")
+        saveFile("report.json")
 
     if !is_undefined(globalParams.seed) {
         shmTreesCmdBuilder.env("SEED", globalParams.seed)