Allow per-library setting for retaining ambiguous features

Author: bbimber

singlecell/resources/chunks/AppendNimble.R

@@ -7,15 +7,16 @@ invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
 # NOTE: this file is created by DownloadAndAppendNimble if there was an error. It might exist if a job failed and then was restarted
-if (file.exists('debug.nimble.txt')) {
-  unlink('debug.nimble.txt')
+if (file.exists('debug.nimble.txt.gz')) {
+  unlink('debug.nimble.txt.gz')
 }
 
 for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
   for (genomeId in names(nimbleGenomes)) {
+    retainAmbiguousFeatures <- !nimbleGenomeAmbiguousPreference[[genomeId]]
     seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, dropAmbiguousFeatures = !retainAmbiguousFeatures, maxLibrarySizeRatio = maxLibrarySizeRatio)
   }
 

singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js

@@ -10,7 +10,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 	initComponent: function(){
 		Ext4.apply(this, {
 			style: 'padding: 10px;margins: 5px;',
-            minWidth: 650,
+            minWidth: 850,
 			border: true,
 			items: [{
 				html: 'This step will query nimble results for the selected genome(s). It will then append these results to the seurat object on the target assay.',
@@ -20,7 +20,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 			},{
 				xtype: 'ldk-gridpanel',
 				clicksToEdit: 1,
-				width: 600,
+				width: 775,
 				tbar: [{
 					text: 'Add',
 					handler: function(btn){
@@ -40,7 +40,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 				},LABKEY.ext4.GRIDBUTTONS.DELETERECORD()],
 				store: {
 					type: 'array',
-					fields: ['genomeId', 'targetAssay']
+					fields: ['genomeId', 'targetAssay','retainAmbiguousFeatures']
 				},
 				columns: [{
 					dataIndex: 'genomeId',
@@ -68,6 +68,14 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 						xtype: 'textfield',
 						allowBlank: false
 					}
+				},{
+					dataIndex: 'retainAmbiguousFeatures',
+					width: 175,
+					header: 'Retain Ambiguous Features?',
+					editor: {
+						xtype: 'checkbox',
+						allowBlank: false
+					}
 				}]
 			}]
 		});
@@ -78,7 +86,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 	getValue: function(){
 		var ret = [];
 		this.down('ldk-gridpanel').store.each(function(r, i) {
-			ret.push([r.data.genomeId, r.data.targetAssay]);
+			ret.push([r.data.genomeId, r.data.targetAssay, !!r.data.retainAmbiguousFeatures]);
 		}, this);
 
 		return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
@@ -113,7 +121,8 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 			Ext4.Array.forEach(val, function(row){
 				var rec = grid.store.createModel({
 					genomeId: row[0],
-					targetAssay: row[1]
+					targetAssay: row[1],
+					retainAmbiguousFeatures: !!row[2]
 				});
 				grid.store.add(rec);
 			}, this);

singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java

@@ -32,10 +32,6 @@ public Provider()
                     {{
                         put("allowBlank", false);
                     }}, null),
-                    SeuratToolParameter.create("retainAmbiguousFeatures", "Retain Ambiguous Features", "If checked, features hitting more than one reference will be retained", "checkbox", new JSONObject()
-                    {{
-                        put("check", false);
-                    }}, false, null, true),
                     SeuratToolParameter.create("ensureSamplesShareAllGenomes", "Ensure Samples Share All Genomes", "If checked, the job will fail unless nimble data is found for each requested genome for all samples", "checkbox", new JSONObject()
                     {{
                         put("check", true);
@@ -76,7 +72,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         for (int i = 0; i < json.length(); i++)
         {
             JSONArray arr = json.getJSONArray(i);
-            if (arr.length() != 2)
+            if (arr.length() != 3)
             {
                 throw new PipelineJobException("Unexpected value: " + json.getString(i));
             }
@@ -88,6 +84,23 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         }
         ret.bodyLines.add(")");
 
+        ret.bodyLines.add("nimbleGenomeAmbiguousPreference <- list(");
+        delim = "";
+        for (int i = 0; i < json.length(); i++)
+        {
+            JSONArray arr = json.getJSONArray(i);
+            if (arr.length() != 3)
+            {
+                throw new PipelineJobException("Unexpected value: " + json.getString(i));
+            }
+
+            int genomeId = arr.getInt(0);
+            boolean retainAmbiguousFeatures = arr.getBoolean(2);
+            ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (retainAmbiguousFeatures ? "TRUE" : "FALSE"));
+            delim = ",";
+        }
+        ret.bodyLines.add(")");
+
         return ret;
     }
 

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -535,9 +535,9 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         return resultMap;
     }
 
-    private File getReportHtmlFileFromResults(File reportResultsGz)
+    private File getReportHtmlFileFromResults(File reportResults)
     {
-        return new File(reportResultsGz.getPath().replaceAll("txt.gz$", "html$"));
+        return new File(reportResults.getPath().replaceAll("txt(.gz)*$", "html"));
     }
 
     private File getNimbleDoneFile(File parentDir, String resumeString)