Dont enforce calling methods for cite-seq only

Author: bbimber

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

@@ -71,7 +71,7 @@ static public void setInstance(CellHashingService instance)
 
     abstract public boolean usesCiteSeq(SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles) throws PipelineJobException;
 
-    abstract public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcludeFailedcDNA);
+    abstract public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcludeFailedcDNA, BARCODE_TYPE type);
 
     abstract public Set<String> getHtosForParentReadset(Integer parentReadsetId, File webserverJobDir, SequenceAnalysisJobSupport support) throws PipelineJobException;
 

singlecell/resources/chunks/Functions.R

@@ -21,7 +21,7 @@ addIntermediateFile <- function(f) { intermediateFiles <<- c(intermediateFiles,
 # This will store any modified/transformed Seurat objects:
 newSeuratObjects <- list()
 
-#print('Updating future.globals.maxSize')
-#options(future.globals.maxSize = Inf)
+print('Updating future.globals.maxSize')
+options(future.globals.maxSize = Inf)
 
 options('Seurat.memsafe' = TRUE)

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

@@ -823,24 +823,29 @@ public void processMetrics(SequenceOutputFile so, PipelineJob job, boolean updat
     }
 
     @Override
-    public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcludeFailedcDNA)
+    public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcludeFailedcDNA, BARCODE_TYPE type)
     {
         List<ToolParameterDescriptor> ret = new ArrayList<>(Arrays.asList(
                 ToolParameterDescriptor.create("scanEditDistances", "Scan Edit Distances", "If checked, CITE-seq-count will be run using edit distances from 0-3 and the iteration with the highest singlets will be used.", "checkbox", new JSONObject(){{
                     put("checked", false);
                 }}, false),
                 ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 2),
-                ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5),
-                ToolParameterDescriptor.create("methods", "Calling Methods", "The set of methods to use in calling.", "ldk-simplecombo", new JSONObject(){{
-                    put("multiSelect", true);
-                    put("allowBlank", false);
-                    put("storeValues", StringUtils.join(Arrays.stream(CALLING_METHOD.values()).map(Enum::name).collect(Collectors.toList()), ";"));
-                    put("initialValues", StringUtils.join(CALLING_METHOD.getDefaultMethodNames(), ";"));
-                    put("delimiter", ";");
-                    put("joinReturnValue", true);
-                }}, null)
+                ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5)
         ));
 
+        if (type == BARCODE_TYPE.hashing)
+        {
+            ret.add(ToolParameterDescriptor.create("methods", "Calling Methods", "The set of methods to use in calling.", "ldk-simplecombo", new JSONObject()
+            {{
+                put("multiSelect", true);
+                put("allowBlank", false);
+                put("storeValues", StringUtils.join(Arrays.stream(CALLING_METHOD.values()).map(Enum::name).collect(Collectors.toList()), ";"));
+                put("initialValues", StringUtils.join(CALLING_METHOD.getDefaultMethodNames(), ";"));
+                put("delimiter", ";");
+                put("joinReturnValue", true);
+            }}, null));
+        }
+
         if (includeExcludeFailedcDNA)
         {
             ret.add(ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, false));

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

@@ -115,7 +115,7 @@ private static List<ToolParameterDescriptor> getDefaultParams()
                 }}, null)
         ));
 
-        ret.addAll(CellHashingService.get().getDefaultHashingParams(false));
+        ret.addAll(CellHashingService.get().getDefaultHashingParams(false, CellHashingService.BARCODE_TYPE.hashing));
 
         return ret;
     }

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

@@ -38,7 +38,7 @@ public LoupeCellHashingHandler()
 
     private static List<ToolParameterDescriptor> getDefaultParams()
     {
-        List<ToolParameterDescriptor> ret = new ArrayList<>(CellHashingService.get().getDefaultHashingParams(true));
+        List<ToolParameterDescriptor> ret = new ArrayList<>(CellHashingService.get().getDefaultHashingParams(true, CellHashingService.BARCODE_TYPE.hashing));
         ret.add(
                 ToolParameterDescriptor.create("useOutputFileContainer", "Submit to Source File Workbook", "If checked, each job will be submitted to the same workbook as the input file, as opposed to submitting all jobs to the same workbook.  This is primarily useful if submitting a large batch of files to process separately. This only applies if 'Run Separately' is selected.", "checkbox", new JSONObject(){{
                     put("checked", true);

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

@@ -40,7 +40,7 @@ private static List<ToolParameterDescriptor> getDefaultParams()
             put("checked", true);
         }}, false));
 
-        ret.addAll(CellHashingService.get().getDefaultHashingParams(true));
+        ret.addAll(CellHashingService.get().getDefaultHashingParams(true, CellHashingService.BARCODE_TYPE.hashing));
 
         return ret;
     }

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

@@ -61,6 +61,7 @@ private static List<ToolParameterDescriptor> getParams()
             put("initialValues", "PCA-tSNE");
         }}, "PCA-tSNE"));
 
+        ret.addAll(CellHashingService.get().getDefaultHashingParams(false, CellHashingService.BARCODE_TYPE.citeseq));
         return ret;
     }
 

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

@@ -32,7 +32,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("RunCellHashing", "Possibly Run/Store Cell Hashing", "cellhashR", "If available, this will run cellhashR to score cells by sample.", CellHashingService.get().getDefaultHashingParams(false), null, null);
+            super("RunCellHashing", "Possibly Run/Store Cell Hashing", "cellhashR", "If available, this will run cellhashR to score cells by sample.", CellHashingService.get().getDefaultHashingParams(false, CellHashingService.BARCODE_TYPE.hashing), null, null);
         }
 
         @Override