Support PBSV call

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java

@@ -87,6 +87,7 @@
 import org.labkey.sequenceanalysis.run.analysis.PARalyzerAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.PangolinHandler;
 import org.labkey.sequenceanalysis.run.analysis.PbsvAnalysis;
+import org.labkey.sequenceanalysis.run.analysis.PbsvJointCallingHandler;
 import org.labkey.sequenceanalysis.run.analysis.PindelAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.SequenceBasedTypingAnalysis;
 import org.labkey.sequenceanalysis.run.analysis.SnpCountAnalysis;
@@ -350,6 +351,7 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new PangolinHandler());
         SequenceAnalysisService.get().registerFileHandler(new NextCladeHandler());
         SequenceAnalysisService.get().registerFileHandler(new ConvertToCramHandler());
+        SequenceAnalysisService.get().registerFileHandler(new PbsvJointCallingHandler());
 
         SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());
         SequenceAnalysisService.get().registerReadsetHandler(new RestoreSraDataHandler());

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java

@@ -0,0 +1,121 @@
+package org.labkey.sequenceanalysis.run.analysis;
+
+import org.json.JSONObject;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.RecordedAction;
+import org.labkey.api.sequenceanalysis.SequenceOutputFile;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
+import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
+import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
+import org.labkey.api.util.FileType;
+import org.labkey.sequenceanalysis.SequenceAnalysisModule;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class PbsvJointCallingHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
+{
+    private static final FileType FILE_TYPE = new FileType(".svsig.gz");
+
+    public PbsvJointCallingHandler()
+    {
+        super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.NAME), "Pbsv Call", "Runs pbsv call, which jointly calls genotypes from PacBio data", null, Arrays.asList(
+                ToolParameterDescriptor.create("fileName", "VCF Filename", "The name of the resulting file.", "textfield", new JSONObject(){{
+                    put("allowBlank", false);
+                    put("doNotIncludeInTemplates", true);
+                }}, null)
+        ));
+    }
+
+    @Override
+    public boolean canProcess(SequenceOutputFile o)
+    {
+        return o.getFile() != null && FILE_TYPE.isType(o.getFile());
+    }
+
+    @Override
+    public boolean doRunRemote()
+    {
+        return true;
+    }
+
+    @Override
+    public boolean doRunLocal()
+    {
+        return false;
+    }
+
+    @Override
+    public SequenceOutputProcessor getProcessor()
+    {
+        return new Processor();
+    }
+
+    public static class Processor implements SequenceOutputProcessor
+    {
+        @Override
+        public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
+        {
+
+        }
+
+        @Override
+        public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
+        {
+            List<String> args = new ArrayList<>();
+            args.add(getExe().getPath());
+            args.add("call");
+
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
+            if (maxThreads != null)
+            {
+                args.add("-j");
+                args.add(String.valueOf(maxThreads));
+            }
+
+            ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenomes().iterator().next();
+            args.add(genome.getWorkingFastaFile().getPath());
+
+            inputFiles.forEach(f -> {
+                args.add(f.getFile().getPath());
+            });
+
+            String fileName = ctx.getParams().getString("fileName");
+            if (!fileName.toLowerCase().endsWith("vcf.gz"))
+            {
+                fileName = fileName + ".vcf.gz";
+            }
+
+            File vcfOut = new File(ctx.getOutputDir(), fileName);
+            args.add(vcfOut.getPath());
+
+            new SimpleScriptWrapper(ctx.getLogger()).execute(args);
+
+            if (!vcfOut.exists())
+            {
+                throw new PipelineJobException("Unable to find file: " + vcfOut.getPath());
+            }
+
+            SequenceOutputFile so = new SequenceOutputFile();
+            so.setName("pbsv call: " + fileName);
+            so.setFile(vcfOut);
+            so.setCategory("PBSV VCF");
+            so.setLibrary_id(genome.getGenomeId());
+
+            ctx.addSequenceOutput(so);
+        }
+
+        private File getExe()
+        {
+            return SequencePipelineService.get().getExeForPackage("PBSVPATH", "pbsv");
+        }
+    }
+}