Avoid NPE

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAnalysisTask.java

@@ -207,7 +207,14 @@ public RecordedActionSet run() throws PipelineJobException
                             getJob().getLogger().warn("Duplicate BAM was: " + d.getFile().getPath());
                         }
 
-                        if (!d.getFile().exists())
+                        //NOTE: if the job was restarted, the BAM might have already been discarded:
+                        if (discardBam && !d.getFile().exists() && d.getFile().getPath().startsWith(getPipelineJob().getWebserverDir(false).getPath()))
+                        {
+                            // Set this value here so downstream steps work. It will be discarded next:
+                            analysisModel.setAlignmentFile(d.getRowId());
+                            found = true;
+                        }
+                        else if (!d.getFile().exists())
                         {
                             getJob().getLogger().warn("BAM registered as output does not exist: " + d.getFile().getPath());
                         }

singlecell/resources/chunks/FindMarkers.R

@@ -2,7 +2,8 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- seuratObjects[[datasetId]]
     seuratObjects[[datasetId]] <- NULL
 
-    dt <- CellMembrane::Find_Markers(seuratObj, identFields = identFields, outFile = paste0(datasetId, '.markers.txt'))
+    outFile = paste0(datasetId, '.markers.txt')
+    dt <- bindArgs(CellMembrane::Find_Markers, seuratObj)
     print(dt)
 
     # Cleanup

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

@@ -34,11 +34,17 @@ public Provider()
                         put("multiSelect", true);
                         put("allowBlank", false);
                         put("storeValues", "wilcox;bimod;roc;t;negbinom;poisson;LR;MAST;DESeq2");
-                        put("initialValues", "wilcox;MAST");
+                        put("initialValues", "wilcox;MAST;DESeq2");
                         put("delimiter", ";");
                         put("joinReturnValue", true);
-                    }}, null)
-            ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+                    }}, null),
+                    SeuratToolParameter.create("pValThreshold", "pVal Threshold", "Only genes with adjusted p-values below this will be reported", "ldk-numberfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 0.001),
+                    SeuratToolParameter.create("foldChangeThreshold", "Log2 Fold-Change Threshold", "Only genes with log2-foldchange above this will be reported", "ldk-numberfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 0.05)
+                ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 
         @Override