Update CheckExpectations and SeuratPrototype steps to include hashing/cite-seq data if needed

Author: bbimber

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

@@ -187,13 +187,13 @@ protected List<Chunk> getChunks(SequenceOutputHandler.JobContext ctx) throws Pip
     }
 
     @Override
-    public boolean requiresHashing()
+    public boolean requiresHashing(SequenceOutputHandler.JobContext ctx)
     {
         return false;
     }
 
     @Override
-    public boolean requiresCiteSeq()
+    public boolean requiresCiteSeq(SequenceOutputHandler.JobContext ctx)
     {
         return false;
     }

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

@@ -29,9 +29,9 @@ default boolean createsSeuratObjects()
         return true;
     }
 
-    public boolean requiresCiteSeq();
+    public boolean requiresCiteSeq(SequenceOutputHandler.JobContext ctx);
 
-    public boolean requiresHashing();
+    public boolean requiresHashing(SequenceOutputHandler.JobContext ctx);
 
     public boolean isIncluded(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputs) throws PipelineJobException;
 

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

@@ -177,12 +177,12 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 SingleCellStep step = stepCtx.getProvider().create(ctx);
                 step.init(ctx, inputFiles);
 
-                if (step.requiresCiteSeq())
+                if (step.requiresCiteSeq(ctx))
                 {
                     requiresCite = true;
                 }
 
-                if (step.requiresHashing())
+                if (step.requiresHashing(ctx))
                 {
                     String methods = step.getProvider().getParameterByName("methods").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), String.class);
                     if (methods != null && methods.contains(CellHashingService.CALLING_METHOD.demuxem.name()))

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

@@ -66,7 +66,7 @@ private static List<ToolParameterDescriptor> getParams()
     }
 
     @Override
-    public boolean requiresCiteSeq()
+    public boolean requiresCiteSeq(SequenceOutputHandler.JobContext ctx)
     {
         return true;
     }

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

@@ -50,6 +50,18 @@ public void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile>
 
     }
 
+    @Override
+    public boolean requiresHashing(SequenceOutputHandler.JobContext ctx)
+    {
+        return getProvider().getParameterByName("requireHashing").extractValue(ctx.getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+    }
+
+    @Override
+    public boolean requiresCiteSeq(SequenceOutputHandler.JobContext ctx)
+    {
+        return getProvider().getParameterByName("requireCiteSeq").extractValue(ctx.getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+    }
+
     @Override
     protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
     {

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

@@ -54,7 +54,7 @@ public RunCellHashing create(PipelineContext ctx)
     }
 
     @Override
-    public boolean requiresHashing()
+    public boolean requiresHashing(SequenceOutputHandler.JobContext ctx)
     {
         return true;
     }

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

@@ -64,6 +64,18 @@ public SeuratPrototype create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public boolean requiresHashing(SequenceOutputHandler.JobContext ctx)
+    {
+        return getProvider().getParameterByName("requireHashing").extractValue(ctx.getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+    }
+
+    @Override
+    public boolean requiresCiteSeq(SequenceOutputHandler.JobContext ctx)
+    {
+        return getProvider().getParameterByName("requireCiteSeq").extractValue(ctx.getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+    }
+
     @Override
     public void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputFiles) throws PipelineJobException
     {