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Add nimble/bulk step
1 parent b084e00 commit 604ee34

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3 files changed

+178
-2
lines changed

3 files changed

+178
-2
lines changed

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

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Original file line numberDiff line numberDiff line change
@@ -114,6 +114,7 @@
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import org.labkey.singlecell.run.CellRangerVDJWrapper;
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import org.labkey.singlecell.run.NimbleAlignmentStep;
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import org.labkey.singlecell.run.NimbleAnalysis;
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import org.labkey.singlecell.run.NimbleBulkAlignmentStep;
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import org.labkey.singlecell.run.RepeatNimbleReportHandler;
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import org.labkey.singlecell.run.VelocytoAlignmentStep;
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import org.labkey.singlecell.run.VelocytoAnalysisStep;
@@ -219,6 +220,7 @@ public static void registerPipelineSteps()
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SequencePipelineService.get().registerPipelineStep(new CellRangerVDJWrapper.VDJProvider());
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SequencePipelineService.get().registerPipelineStep(new NimbleAlignmentStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new NimbleAnalysis.Provider());
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SequencePipelineService.get().registerPipelineStep(new NimbleBulkAlignmentStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new VelocytoAlignmentStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new VelocytoAnalysisStep.Provider());
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‎singlecell/src/org/labkey/singlecell/run/NimbleAnalysis.java‎

Lines changed: 13 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,8 @@
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package org.labkey.singlecell.run;
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import htsjdk.samtools.SAMFileHeader;
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import htsjdk.samtools.SAMTag;
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import htsjdk.samtools.SamReaderFactory;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.model.AnalysisModel;
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import org.labkey.api.sequenceanalysis.model.Readset;
@@ -29,7 +32,7 @@ public static class Provider extends AbstractAnalysisStepProvider<NimbleAnalysis
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{
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public Provider()
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{
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super("NimbleAnalysis", "Nimble", null, "This will run Nimble to generate a supplemental feature count matrix for the provided libraries", NimbleAlignmentStep.getToolParameters(), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null);
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super("NimbleAnalysis", "Nimble", null, "This will run Nimble to generate a supplemental feature count matrix for the provided libraries. This should work using either CellRanger/scRNA-seq or bulk input data.", NimbleAlignmentStep.getToolParameters(), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null);
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}
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@Override
@@ -58,7 +61,15 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
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NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
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helper.doNimbleAlign(inputBam, output, rs, FileUtil.getBaseName(inputBam));
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NimbleHelper.write10xBarcodes(inputBam, getPipelineCtx().getLogger(), rs, referenceGenome, output);
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SAMFileHeader header = SamReaderFactory.makeDefault().getFileHeader(inputBam);
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if (header.getAttribute(SAMTag.CB.name()) != null)
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{
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NimbleHelper.write10xBarcodes(inputBam, getPipelineCtx().getLogger(), rs, referenceGenome, output);
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}
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else
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{
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getPipelineCtx().getLogger().info("BAM lacks CB tag, will not output 10x barcodes to file");
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}
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return output;
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}

‎singlecell/src/org/labkey/singlecell/run/NimbleBulkAlignmentStep.java‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,163 @@
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package org.labkey.singlecell.run;
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import org.apache.logging.log4j.Logger;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.model.Readset;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractAnalysisStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl;
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import org.labkey.api.sequenceanalysis.pipeline.AlignmentStep;
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import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
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import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.sequenceanalysis.run.AbstractAlignmentPipelineStep;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.util.PageFlowUtil;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.LinkedHashSet;
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import java.util.List;
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public class NimbleBulkAlignmentStep extends AbstractAlignmentPipelineStep<NimbleBulkAlignmentStep.NimbleBulkWrapper> implements AlignmentStep
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{
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public static class Provider extends AbstractAnalysisStepProvider<NimbleAnalysis>
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{
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public Provider()
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{
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super("NimbleBulkAnalysis", "Nimble (Bulk)", null, "This will run Nimble to generate a supplemental feature count matrix for the provided libraries. This version is intended for bulk input data. Please use the CellRanger/Nimble version for scRNA-seq", NimbleAlignmentStep.getToolParameters(), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null);
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}
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@Override
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public NimbleAnalysis create(PipelineContext ctx)
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{
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return new NimbleAnalysis(this, ctx);
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}
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}
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public NimbleBulkAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx, NimbleBulkAlignmentStep.NimbleBulkWrapper wrapper)
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{
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super(provider, ctx, wrapper);
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}
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@Override
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public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir) throws PipelineJobException
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{
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return null;
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}
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@Override
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public void init(SequenceAnalysisJobSupport support) throws PipelineJobException
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{
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NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
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List<Integer> genomeIds = helper.getGenomeIds();
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for (int id : genomeIds)
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{
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helper.prepareGenome(id);
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}
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}
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@Override
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public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
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{
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AlignmentOutputImpl output = new AlignmentOutputImpl();
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SamtoolsRunner st = new SamtoolsRunner(getPipelineCtx().getLogger());
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List<File> outputBams = new ArrayList<>();
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int bamIdx = 0;
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while (bamIdx < inputFastqs1.size())
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{
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File outputBam = new File(getPipelineCtx().getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped." + bamIdx + ".bam");
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List<String> args = new ArrayList<>(Arrays.asList(st.getSamtoolsPath().getPath(), "import", "-o", outputBam.getPath(), "-r", "ID:" + readGroupId));
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if (inputFastqs2 == null || inputFastqs2.isEmpty())
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{
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args.add("-O");
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args.add(inputFastqs1.get(bamIdx).getPath());
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}
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else
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{
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args.add("-1");
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args.add(inputFastqs1.get(bamIdx).getPath());
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if (bamIdx > inputFastqs2.size())
89+
{
90+
throw new PipelineJobException("Unequal lengths for first/second pair FASTQs");
91+
}
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93+
args.add("-2");
94+
args.add(inputFastqs2.get(bamIdx).getPath());
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}
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bamIdx++;
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st.execute(args);
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outputBams.add(outputBam);
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}
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File outputBam;
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if (outputBams.size() > 1)
104+
{
105+
outputBam = new File(getPipelineCtx().getWorkingDirectory(), FileUtil.makeLegalName(rs.getName()) + ".unmapped.bam");
106+
outputBams.forEach(output::addIntermediateFile);
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108+
List<String> args = new ArrayList<>(Arrays.asList(st.getSamtoolsPath().getPath(), "merge", "-o", outputBam.getPath(), "-f"));
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Integer maxThreads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
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if (maxThreads != null)
111+
{
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args.add("-@");
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args.add(maxThreads.toString());
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}
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116+
outputBams.forEach(bam -> args.add(bam.getPath()));
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st.execute(args);
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}
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else
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{
121+
outputBam = outputBams.get(0);
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}
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124+
// Now run nimble itself:
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NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
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helper.doNimbleAlign(outputBam, output, rs, basename);
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output.setBAM(outputBam);
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return output;
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}
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@Override
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public boolean doAddReadGroups()
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{
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return false;
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}
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@Override
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public boolean doSortIndexBam()
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{
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return false;
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}
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@Override
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public boolean alwaysCopyIndexToWorkingDir()
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{
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return false;
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}
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@Override
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public boolean supportsGzipFastqs()
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{
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return true;
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}
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public static class NimbleBulkWrapper extends AbstractCommandWrapper
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{
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public NimbleBulkWrapper(Logger log)
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{
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super(log);
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}
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}
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}

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