Delete MS2 GWT code. Switch to simple job launcher (#479)

Author: labkey-jeckels

nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java

@@ -1,14 +1,13 @@
 package org.labkey.nextflow.pipeline;
 
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocol;
 import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
 import org.labkey.api.util.FileType;
 import org.labkey.api.view.ViewBackgroundInfo;
 
-import java.io.File;
-import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
@@ -42,7 +41,7 @@ public AbstractFileAnalysisProtocolFactory<NextFlowProtocol> getFactory()
         return new AbstractFileAnalysisProtocolFactory<>()
         {
             @Override
-            public NextFlowProtocol createProtocolInstance(String name, String description, String xml)
+            public NextFlowProtocol createProtocolInstance(String name, String description, String xml, Container container)
             {
                 return new NextFlowProtocol();
             }
@@ -62,7 +61,7 @@ public String getName()
     }
 
     @Override
-    public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<File> filesInput, File fileParameters, @Nullable Map<String, String> variableMap) throws IOException
+    public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<Path> filesInput, Path fileParameters, @Nullable Map<String, String> variableMap)
     {
         throw new UnsupportedOperationException();
     }