@platforma-open/milaboratories.mixcr-shm-trees.workflow 2.3.0 → 2.3.2

package/CHANGELOG.md

@@ -1,5 +1,20 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 2.3.2
+
+### Patch Changes
+
+- 7efd2ac: Allele seed changed
+
+## 2.3.1
+
+### Patch Changes
+
+- 1edb8af: - Fix for column name "Number of clones" -> "Number of nodes"
+  - Added "Distance to parent" column
+  - "Distance to parent" column is now used as distance measure for tree visualization by default
+  - Assembling feature (i.e. VDJRegion) is added as individual export column
+
 ## 2.3.0
 
 ### Minor Changes

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

@@ -101,7 +101,7 @@ shmTreeTableOptions := func(dataDescription) {
             "name": "pl7.app/vdj/numberOfNodesWithClones",
             "valueType": "Long",
             "annotations": {
-                "pl7.app/label": "Number of clones"
+                "pl7.app/label": "Number of nodes"
             }
         }
     })
@@ -306,8 +306,31 @@ shmTreeNodesTableOptions := func(dataDescription) {
         "spec": {
             "name": "pl7.app/dendrogram/distance",
             "valueType": "Double",
+            "domain": {
+                "pl7.app/dendrogram/distance/from": "germline"
+            },
             "annotations": {
                 "pl7.app/label": "Distanse from germline",
+                "pl7.app/dendrogram/distance/from": "germline", // change to domain only, once can be selected in graphmaker
+                "pl7.app/dendrogram/isDistance": "true"
+            }
+        }
+    })
+
+    cmdArgs = append(cmdArgs, "-distance", "parent")
+    columns = append(columns, {
+        "column": "DistanceFromParent",
+        "id": "distance-from-parent",
+        "allowNA": true,
+        "spec": {
+            "name": "pl7.app/dendrogram/distance",
+            "valueType": "Double",
+            "domain": {
+                "pl7.app/dendrogram/distance/from": "parent"
+            },
+            "annotations": {
+                "pl7.app/label": "Distanse from parent",
+                "pl7.app/dendrogram/distance/from": "parent", // change to domain only, once can be selected in graphmaker
                 "pl7.app/dendrogram/isDistance": "true"
             }
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "2.3.0",
+  "version": "2.3.2",
   "type": "module",
   "description": "Tengo-based template",
   "//": {

package/src/export-settings.lib.tengo

@@ -101,7 +101,7 @@ shmTreeTableOptions := func(dataDescription) {
             "name": "pl7.app/vdj/numberOfNodesWithClones",
             "valueType": "Long",
             "annotations": {
-                "pl7.app/label": "Number of clones"
+                "pl7.app/label": "Number of nodes"
             }
         }
     })
@@ -306,8 +306,31 @@ shmTreeNodesTableOptions := func(dataDescription) {
         "spec": {
             "name": "pl7.app/dendrogram/distance",
             "valueType": "Double",
+            "domain": {
+                "pl7.app/dendrogram/distance/from": "germline"
+            },
             "annotations": {
                 "pl7.app/label": "Distanse from germline",
+                "pl7.app/dendrogram/distance/from": "germline", // change to domain only, once can be selected in graphmaker
+                "pl7.app/dendrogram/isDistance": "true"
+            }
+        }
+    })
+
+    cmdArgs = append(cmdArgs, "-distance", "parent")
+    columns = append(columns, {
+        "column": "DistanceFromParent",
+        "id": "distance-from-parent",
+        "allowNA": true,
+        "spec": {
+            "name": "pl7.app/dendrogram/distance",
+            "valueType": "Double",
+            "domain": {
+                "pl7.app/dendrogram/distance/from": "parent"
+            },
+            "annotations": {
+                "pl7.app/label": "Distanse from parent",
+                "pl7.app/dendrogram/distance/from": "parent", // change to domain only, once can be selected in graphmaker
                 "pl7.app/dendrogram/isDistance": "true"
             }
         }

package/src/process.tpl.tengo

@@ -52,12 +52,15 @@ self.body(func(inputs) {
 		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 == "") {
-			assemblingFeature = dataDescription["mixcr.com/assemblingFeature"]
-		} else if (assemblingFeature != dataDescription["mixcr.com/assemblingFeature"]) {
-			ll.panic("Assmble features should be the same to process tress. Got " + assemblingFeature + " and " + dataDescription["mixcr.com/assemblingFeature"])
+			assemblingFeature = presetAnnotations["mixcr.com/assemblingFeature"]
+		} else if (assemblingFeature != presetAnnotations["mixcr.com/assemblingFeature"]) {
+			ll.panic("Assmble features should be the same to process tress. Got " + assemblingFeature + " and " + presetAnnotations["mixcr.com/assemblingFeature"])
 		}
 	}
 
+	// adding assembling feature to the list of covered features
+	dataDescription.coveredFeatures = append(dataDescription.coveredFeatures, assemblingFeature)
+
 	// there should be call join on pfFrames, but it's not implements, so we will do it by hand
 	dataGroupedByDonorId := prepareDonorColumn.groupDataByDonorId(inputs.donorColumn, inputs.datasets)
 

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

@@ -36,6 +36,7 @@ self.body(func(inputs) {
         printErrStreamToStdout().
         secret("MI_LICENSE", "MI_LICENSE").
         env("MI_PROGRESS_PREFIX", progressPrefix).
+        env("SEED", "1").
         software(mixcrSw).
         arg("findAlleles").
         arg("--report").arg("report.txt").