Reduce length of filenames in single cell pipelines

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java

@@ -36,6 +36,11 @@ default boolean createsSeuratObjects()
 
     public boolean isIncluded(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputs) throws PipelineJobException;
 
+    default String getFileSuffix()
+    {
+        return getProvider().getName();
+    }
+
     public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException;
 
     public static interface Output extends PipelineStepOutput

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

@@ -322,7 +322,7 @@ else if (step.createsSeuratObjects())
                 currentFiles.forEach(currentFile -> action.addInput(currentFile.getFile(), "Input Seurat Object"));
                 ctx.getFileManager().addIntermediateFiles(currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).collect(Collectors.toList()));
 
-                outputPrefix = outputPrefix + "." + step.getProvider().getName() + (step.getStepIdx() == 0 ? "" : "-" + step.getStepIdx());
+                outputPrefix = outputPrefix + "." + step.getFileSuffix() + (step.getStepIdx() == 0 ? "" : "-" + step.getStepIdx());
                 SingleCellStep.Output output = step.execute(ctx, currentFiles, outputPrefix);
 
                 _resumer.getFileManager().addStepOutputs(action, output);

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

@@ -61,6 +61,12 @@ private static List<ToolParameterDescriptor> getParams()
         return ret;
     }
 
+    @Override
+    public String getFileSuffix()
+    {
+        return "cite";
+    }
+
     @Override
     public Collection<String> getRLibraries()
     {

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

@@ -33,6 +33,12 @@ public AvgExpression create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public String getFileSuffix()
+    {
+        return "avg";
+    }
+
     @Override
     public boolean createsSeuratObjects()
     {

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

@@ -28,4 +28,10 @@ public CiteSeqDimRedux create(PipelineContext ctx)
             return new CiteSeqDimRedux(ctx, this);
         }
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "cite-dr";
+    }
 }

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

@@ -28,4 +28,10 @@ public CiteSeqWnn create(PipelineContext ctx)
             return new CiteSeqWnn(ctx, this);
         }
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "wnn";
+    }
 }

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

@@ -49,4 +49,10 @@ public boolean createsSeuratObjects()
     {
         return false;
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "dimplot";
+    }
 }

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

@@ -32,4 +32,10 @@ public DoubletFinder create(PipelineContext ctx)
             return new DoubletFinder(ctx, this);
         }
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "df";
+    }
 }

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

@@ -39,4 +39,10 @@ public Downsample create(PipelineContext ctx)
             return new Downsample(ctx, this);
         }
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "ds";
+    }
 }

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

@@ -50,4 +50,10 @@ public FilterRawCounts create(PipelineContext ctx)
             return new FilterRawCounts(ctx, this);
         }
     }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "frc";
+    }
 }