Generate CITE-seq as unfiltered table

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/BaseSequencePanel.js

@@ -11,8 +11,8 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
 
     initComponent: function(){
         //NOTE: if we're in a workbook, default to serch against the parent, since it will include children by default
-        this.queryContainer = LABKEY.Security.currentContainer.type == 'workbook' ? LABKEY.Security.currentContainer.parentId : LABKEY.Security.currentContainer.id;
-        this.queryContainerPath = LABKEY.Security.currentContainer.type == 'workbook' ? LABKEY.Security.currentContainer.parentPath : LABKEY.Security.currentContainer.path;
+        this.queryContainer = LABKEY.Security.currentContainer.type === 'workbook' ? LABKEY.Security.currentContainer.parentId : LABKEY.Security.currentContainer.id;
+        this.queryContainerPath = LABKEY.Security.currentContainer.type === 'workbook' ? LABKEY.Security.currentContainer.parentPath : LABKEY.Security.currentContainer.path;
 
         this.initFiles();
 
@@ -330,6 +330,13 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
                         sequencePanel: this
                     }).show(btn);
                 }
+            },{
+                xtype: 'ldk-linkbutton',
+                text: 'Manage Saved Templates',
+                linkCls: 'labkey-text-link',
+                linkTarget: LABKEY.ActionURL.buildURL('query', 'executeQuery', Laboratory.Utils.getQueryContainerPath(), {schemaName: 'sequenceanalysis', 'query.queryName': 'saved_analyses', 'query.jobType~eq': this.jobType}),
+                visible: LABKEY.Security.currentUser.isAdmin,
+                scope: this
             }]
         }
     },

singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java

@@ -96,6 +96,7 @@ public static class CellHashingParameters
         public Integer minCountPerCell = 5;
         public List<CALLING_METHOD> methods = CALLING_METHOD.getDefaultMethods();
         public String basename = null;
+        public Integer cells = 0;
 
         private CellHashingParameters()
         {

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -363,7 +363,7 @@ public File processCellHashingOrCiteSeqForParent(Readset parentReadset, Pipeline
         }
 
         ctx.getLogger().debug("total cached readset/" + parameters.type.name() + " readset pairs: " + readsetToHashingOrCite.size());
-        ctx.getLogger().debug("unique HTOs: " + lineCount);
+        ctx.getLogger().debug("unique indexes: " + lineCount);
 
         Readset htoOrCiteReadset = ctx.getSequenceSupport().getCachedReadset(readsetToHashingOrCite.get(parentReadset.getReadsetId()));
         if (htoOrCiteReadset == null)
@@ -1358,7 +1358,7 @@ public Map<String, Object> executeCiteSeqCount(File outputDir, String basename,
                 //Note: version 1.4.2 and greater requires this:
                 //https://github.com/Hoohm/CITE-seq-Count/issues/56
                 baseArgs.add("-cells");
-                baseArgs.add("0");
+                baseArgs.add(parameters.cells == null ? "0" : String.valueOf(parameters.cells));
             }
 
             Integer cores = SequencePipelineService.get().getMaxThreads(log);

singlecell/src/org/labkey/singlecell/analysis/ProcessSingleCellHandler.java

@@ -278,7 +278,6 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             for (PipelineStepCtx<SingleCellStep> stepCtx : steps)
             {
                 ctx.getLogger().info("Starting to run: " + stepCtx.getProvider().getLabel());
-                ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running: " + stepCtx.getProvider().getLabel());
                 stepIdx++;
 
                 SingleCellStep step = stepCtx.getProvider().create(ctx);
@@ -309,6 +308,7 @@ else if (step.createsSeuratObjects())
                     continue;
                 }
 
+                ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running: " + stepCtx.getProvider().getLabel());
                 currentFiles.forEach(currentFile -> {
                     if (currentFile.getSequenceOutputFileId() != null)
                     {

singlecell/src/org/labkey/singlecell/button/CiteSeqButton.java

@@ -16,7 +16,7 @@ public class CiteSeqButton extends SimpleButtonConfigFactory
 {
     public CiteSeqButton()
     {
-        super(ModuleLoader.getInstance().getModule(SingleCellModule.class), "Generate CITE-seq Table", "SequenceAnalysis.window.OutputHandlerWindow.readsetButtonHandler(dataRegionName, '" + CiteSeqHandler.class.getName() + "');",
+        super(ModuleLoader.getInstance().getModule(SingleCellModule.class), "Generate CITE-seq Count Table", "SequenceAnalysis.window.OutputHandlerWindow.readsetButtonHandler(dataRegionName, '" + CiteSeqHandler.class.getName() + "');",
                 Arrays.asList(
                         ClientDependency.supplierFromModuleName("ldk"),
                         ClientDependency.supplierFromModuleName("laboratory"),

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

@@ -107,6 +107,7 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO
                 params.createOutputFiles = true;
                 params.genomeId = wrapper.getSequenceOutputFile().getLibrary_id();
                 params.cellBarcodeWhitelistFile = cellBarcodesParsed;
+                params.cells = 250000;
 
                 finalOutput = CellHashingService.get().processCellHashingOrCiteSeqForParent(parentReadset, output, ctx, params);
             }