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Support vireo
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2 files changed

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‎singlecell/src/org/labkey/singlecell/SingleCellModule.java‎

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@@ -172,6 +172,7 @@ public static void registerPipelineSteps()
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SequencePipelineService.get().registerPipelineStep(new ClrNormalizeByGroup.Provider());
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SequenceAnalysisService.get().registerFileHandler(new CellRangerVLoupeRepairHandler());
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SequencePipelineService.get().registerPipelineStep(new PrepareRawCounts.Provider());
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SequenceAnalysisService.get().registerFileHandler(new VireoHandler());
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SequencePipelineService.get().registerPipelineStep(new RemoveCellCycle.Provider());
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SequencePipelineService.get().registerPipelineStep(new RunCellHashing.Provider());

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

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package org.labkey.singlecell.pipeline.singlecell;
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import htsjdk.samtools.util.IOUtil;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.lang3.StringUtils;
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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.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
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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.writer.PrintWriters;
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import org.labkey.singlecell.SingleCellModule;
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import org.labkey.singlecell.run.CellRangerGexCountStep;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.IOException;
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import java.io.PrintWriter;
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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 VireoHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
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{
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public VireoHandler()
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{
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super(ModuleLoader.getInstance().getModule(SingleCellModule.class), "Run Vireo", "This will run cellsnp-lite and vireo to infer cell-to-sample based on genotype.", null, Arrays.asList(
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ToolParameterDescriptor.create("nDonors", "# Donors", "The number of donors to demultiplex", "ldk-integerfield", new JSONObject(){{
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put("allowBlank", false);
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}}, null),
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ToolParameterDescriptor.create("contigs", "Allowable Contigs", "A comma-separated list of contig names to use", "textfield", new JSONObject(){{
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}}, "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20")
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));
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}
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@Override
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public boolean doSplitJobs()
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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 canProcess(SequenceOutputFile o)
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{
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return CellRangerGexCountStep.LOUPE_CATEGORY.equals(o.getCategory()) & o.getFile().getName().endsWith("cloupe.cloupe");
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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 Processor();
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}
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public class Processor implements SequenceOutputProcessor
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{
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@Override
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public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
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{
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if (inputFiles.size() > 1)
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{
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throw new PipelineJobException("Expected a single input");
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}
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File bc = getBarcodesFile(inputFiles.get(0).getFile());
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if (!bc.exists())
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{
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throw new PipelineJobException("Unable to find file: " + bc.getPath());
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}
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File bam = getBamFile(inputFiles.get(0).getFile());
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if (!bam.exists())
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{
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throw new PipelineJobException("Unable to find file: " + bam.getPath());
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}
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}
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private File getBarcodesFile(File loupe)
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{
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return new File(loupe.getParentFile(), "filtered_feature_bc_matrix/barcodes.tsv.gz");
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}
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private File getBamFile(File loupe)
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{
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File[] files = loupe.getParentFile().getParentFile().listFiles(f -> f.getName().endsWith(".bam"));
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if (files == null || files.length == 0)
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{
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throw new IllegalArgumentException("Unable to find BAM file for Loupe file");
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}
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else if (files.length > 1)
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{
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throw new IllegalArgumentException("More than one possible BAM file found");
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}
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return files[0];
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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 barcodesGz = getBarcodesFile(inputFiles.get(0).getFile());
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File bam = getBamFile(inputFiles.get(0).getFile());
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File barcodes = new File(ctx.getWorkingDirectory(), "barcodes.csv");
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try (BufferedReader reader = IOUtil.openFileForBufferedUtf8Reading(barcodesGz); PrintWriter writer = PrintWriters.getPrintWriter(barcodes))
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{
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String line;
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while ((line = reader.readLine()) != null)
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{
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writer.println(line);
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}
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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().addIntermediateFile(barcodes);
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List<String> cellsnp = new ArrayList<>();
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cellsnp.add("cellsnp-lite");
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cellsnp.add("-s");
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cellsnp.add(bam.getPath());
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cellsnp.add("-b");
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cellsnp.add(barcodes.getPath());
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File cellsnpDir = new File(ctx.getWorkingDirectory(), "cellsnp");
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if (cellsnpDir.exists())
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{
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try
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{
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FileUtils.deleteDirectory(cellsnpDir);
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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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}
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cellsnp.add("-O");
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cellsnp.add(cellsnpDir.getPath());
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Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
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if (maxThreads != null)
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{
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cellsnp.add("-p");
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cellsnp.add(maxThreads.toString());
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}
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cellsnp.add("--minMAF");
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cellsnp.add("0.1");
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cellsnp.add("--minCOUNT");
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cellsnp.add("100");
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cellsnp.add("--gzip");
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ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(inputFiles.get(0).getLibrary_id());
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cellsnp.add("--refseq");
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cellsnp.add(genome.getWorkingFastaFile().getPath());
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String contigs = ctx.getParams().optString("contigs", "");
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if (!StringUtils.isEmpty(contigs))
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{
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cellsnp.add("--chrom");
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cellsnp.add(contigs);
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}
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new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);
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List<String> vireo = new ArrayList<>();
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vireo.add("vireo");
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vireo.add("-c");
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vireo.add(cellsnpDir.getPath());
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if (maxThreads != null)
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{
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vireo.add("-p");
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vireo.add(maxThreads.toString());
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}
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vireo.add("-o");
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vireo.add(ctx.getWorkingDirectory().getPath());
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int nDonors = ctx.getParams().optInt("nDonors", 0);
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if (nDonors == 0)
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{
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throw new PipelineJobException("Must provide nDonors");
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}
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vireo.add("-N");
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vireo.add(String.valueOf(nDonors));
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new SimpleScriptWrapper(ctx.getLogger()).execute(vireo);
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File[] outFiles = ctx.getWorkingDirectory().listFiles(f -> f.getName().endsWith("_donor_ids.tsv"));
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if (outFiles == null || outFiles.length == 0)
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{
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throw new PipelineJobException("Missing vireo output file");
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}
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else if (outFiles.length > 1)
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{
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throw new PipelineJobException("More than one possible vireo output file found");
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}
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SequenceOutputFile so = new SequenceOutputFile();
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so.setReadset(inputFiles.get(0).getReadset());
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so.setLibrary_id(inputFiles.get(0).getLibrary_id());
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so.setFile(outFiles[0]);
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if (so.getReadset() != null)
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{
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so.setName(ctx.getSequenceSupport().getCachedReadset(so.getReadset()).getName() + ": Vireo Demultiplexing");
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}
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else
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{
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so.setName(inputFiles.get(0).getName() + ": Vireo Demultiplexing");
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}
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so.setCategory("Vireo Demultiplexing");
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ctx.addSequenceOutput(so);
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}
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}
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}

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