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Inital support for paraGRAPH
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‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java‎

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import org.labkey.sequenceanalysis.run.alignment.BowtieWrapper;
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import org.labkey.sequenceanalysis.run.alignment.GSnapWrapper;
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import org.labkey.sequenceanalysis.run.alignment.MosaikWrapper;
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import org.labkey.sequenceanalysis.run.alignment.ParagraphStep;
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import org.labkey.sequenceanalysis.run.alignment.Pbmm2Wrapper;
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import org.labkey.sequenceanalysis.run.alignment.StarWrapper;
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import org.labkey.sequenceanalysis.run.alignment.VulcanWrapper;
@@ -336,6 +337,7 @@ public static void registerPipelineSteps()
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SequenceAnalysisService.get().registerFileHandler(new PbsvJointCallingHandler());
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SequenceAnalysisService.get().registerFileHandler(new DeepVariantHandler());
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SequenceAnalysisService.get().registerFileHandler(new GLNexusHandler());
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SequenceAnalysisService.get().registerFileHandler(new ParagraphStep());
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SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());
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SequenceAnalysisService.get().registerReadsetHandler(new RestoreSraDataHandler());

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java‎

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package org.labkey.sequenceanalysis.run.alignment;
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import org.json.JSONObject;
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import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.pipeline.PipelineJob;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.pipeline.RecordedAction;
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import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
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import org.labkey.api.sequenceanalysis.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
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import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
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import org.labkey.api.util.FileUtil;
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import org.labkey.sequenceanalysis.SequenceAnalysisModule;
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import org.labkey.sequenceanalysis.run.variant.DepthOfCoverageHandler;
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import org.labkey.sequenceanalysis.util.SequenceUtil;
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import java.io.File;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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public class ParagraphStep extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
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{
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public ParagraphStep()
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{
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super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Paragraph SV Genotyping", "This will run paraGRAPH on one or more BAM files to genotype SVs", null, Arrays.asList(
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ToolParameterDescriptor.createExpDataParam("svVCF", "Input VCF", "This is the DataId of the VCF containing the SVs to genotype", "ldk-expdatafield", new JSONObject()
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{{
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put("allowBlank", false);
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}}, null)
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));
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}
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@Override
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public boolean canProcess(SequenceOutputFile o)
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{
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return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().isType(o.getFile());
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}
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@Override
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public boolean doRunRemote()
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{
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return true;
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}
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@Override
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public boolean doRunLocal()
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{
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return false;
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}
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@Override
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public SequenceOutputProcessor getProcessor()
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{
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return new DepthOfCoverageHandler.Processor();
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}
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public static class Processor implements SequenceOutputProcessor
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{
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@Override
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public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
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{
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}
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@Override
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public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
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{
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File inputVCF = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("svVCF"));
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if (!inputVCF.exists())
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{
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throw new PipelineJobException("Unable to find file: " + inputVCF.getPath());
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}
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for (SequenceOutputFile so : inputFiles)
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{
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List<String> depthArgs = new ArrayList<>();
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depthArgs.add("idxdepth");
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depthArgs.add("-d");
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depthArgs.add(so.getFile().getPath());
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File coverageFile = new File(ctx.getWorkingDirectory(), "coverage.txt");
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depthArgs.add("-o");
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depthArgs.add(coverageFile.getPath());
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depthArgs.add("-r");
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depthArgs.add(ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile().getPath());
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new SimpleScriptWrapper(ctx.getLogger()).execute(depthArgs);
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if (!coverageFile.exists())
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{
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throw new PipelineJobException("Missing file: " + coverageFile.getPath());
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}
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// Should produce a simple text file:
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// id path depth read length
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// TNPRC-IB18 ../IB18.cram 29.77 150
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List<String> paragraphArgs = new ArrayList<>();
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paragraphArgs.add("multigrmpy.py");
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paragraphArgs.add("--verbose");
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File paragraphOut = new File(ctx.getWorkingDirectory(), FileUtil.getBaseName(so.getFile()) + ".paragraph.txt");
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paragraphArgs.add("-o");
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paragraphArgs.add(paragraphOut.getPath());
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int svVcfId = ctx.getParams().optInt("svVCF");
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if (svVcfId == 0)
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{
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throw new PipelineJobException("Missing svVCF ID");
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}
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File svVcf = ctx.getSequenceSupport().getCachedData(svVcfId);
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if (svVcf == null)
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{
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throw new PipelineJobException("File not found for ID: " + svVcfId);
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}
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else if (!svVcf.exists())
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{
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throw new PipelineJobException("Missing file: " + svVcf.getPath());
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}
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paragraphArgs.add("-i");
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paragraphArgs.add(svVcf.getPath());
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paragraphArgs.add("-m");
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paragraphArgs.add(coverageFile.getPath());
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paragraphArgs.add("-r");
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paragraphArgs.add(ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id()).getWorkingFastaFile().getPath());
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paragraphArgs.add("--scratch-dir");
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paragraphArgs.add(SequencePipelineService.get().getJavaTempDir());
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Integer threads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
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if (threads != null)
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{
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paragraphArgs.add("--threads");
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paragraphArgs.add(threads.toString());
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}
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paragraphArgs.add("--logfile");
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paragraphArgs.add(new File(ctx.getWorkingDirectory(), "paragraph.log").getPath());
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new SimpleScriptWrapper(ctx.getLogger()).execute(paragraphArgs);
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File genotypes = new File(ctx.getWorkingDirectory(), "genotypes.vcf.gz");
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if (!genotypes.exists())
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{
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throw new PipelineJobException("Missing file: " + genotypes.getPath());
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}
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try
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{
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SequenceAnalysisService.get().ensureVcfIndex(genotypes, ctx.getLogger());
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}
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catch (IOException e)
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{
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throw new PipelineJobException(e);
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}
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ctx.getFileManager().addSequenceOutput(genotypes, "paraGRAPH Genotypes: " + so.getName(), "paraGRAPH Genoypes", so.getReadset(), null, so.getLibrary_id(), "Input VCF: " + svVcf.getName() + " (" + svVcfId + ")");
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}
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}
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}
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}

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