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Support Graphtyper
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4 files changed

+166
-2
lines changed

4 files changed

+166
-2
lines changed

‎SequenceAnalysis/pipeline_code/extra_tools_install.sh‎

Lines changed: 14 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -291,4 +291,17 @@ then
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ln -s $SVTYPER ${LKTOOLS_DIR}/svtyper-sso
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else
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echo "Already installed"
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fi
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fi
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if [[ ! -e ${LKTOOLS_DIR}/graphtyper || ! -z $FORCE_REINSTALL ]];
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then
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echo "Cleaning up previous installs"
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rm -Rf $LKTOOLS_DIR/graphtyper*
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wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.7/graphtyper
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chmod a+x graphtyper
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mv ./graphtyper $LKTOOLS_DIR/
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else
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echo "Already installed"
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fi

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

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -98,6 +98,7 @@
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import org.labkey.sequenceanalysis.run.alignment.Bowtie2Wrapper;
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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.Graphtyper;
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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;
@@ -405,6 +406,7 @@ public static void registerPipelineSteps()
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SequenceAnalysisService.get().registerFileHandler(new GLNexusHandler());
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SequenceAnalysisService.get().registerFileHandler(new ParagraphStep());
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SequenceAnalysisService.get().registerFileHandler(new SVTyperStep());
409+
SequenceAnalysisService.get().registerFileHandler(new Graphtyper());
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SequenceAnalysisService.get().registerFileHandler(new UpdateReadsetFilesHandler());
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SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());

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

Lines changed: 149 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,149 @@
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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.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.AbstractCommandWrapper;
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import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
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import org.labkey.sequenceanalysis.SequenceAnalysisModule;
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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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//https://github.com/hall-lab/svtyper
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public class Graphtyper extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
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{
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public Graphtyper()
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{
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super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Graphtyper (SV Genotyping)", "This will run Graphtyper 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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ToolParameterDescriptor.create("useOutputFileContainer", "Submit to Source File Workbook", "If checked, each job will be submitted to the same workbook as the input file, as opposed to submitting all jobs to the same workbook. This is primarily useful if submitting a large batch of files to process separately. This only applies if 'Run Separately' is selected.", "checkbox", new JSONObject(){{
39+
put("checked", true);
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}}, true)
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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)
52+
{
53+
return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bamOrCram.getFileType().isType(o.getFile());
54+
}
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@Override
57+
public boolean doRunRemote()
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{
59+
return true;
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}
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@Override
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public boolean doRunLocal()
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{
65+
return false;
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}
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@Override
69+
public SequenceOutputProcessor getProcessor()
70+
{
71+
return new Processor();
72+
}
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public static class Processor implements SequenceOutputProcessor
75+
{
76+
@Override
77+
public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
78+
{
79+
80+
}
81+
82+
@Override
83+
public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
84+
{
85+
int svVcfId = ctx.getParams().optInt("svVCF", 0);
86+
if (svVcfId == 0)
87+
{
88+
throw new PipelineJobException("svVCF param was null");
89+
}
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91+
File svVcf = ctx.getSequenceSupport().getCachedData(svVcfId);
92+
if (svVcf == null)
93+
{
94+
throw new PipelineJobException("File not found for ID: " + svVcfId);
95+
}
96+
else if (!svVcf.exists())
97+
{
98+
throw new PipelineJobException("Missing file: " + svVcf.getPath());
99+
}
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101+
Integer threads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
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103+
for (SequenceOutputFile so : inputFiles)
104+
{
105+
List<String> args = new ArrayList<>();
106+
SimpleScriptWrapper wrapper = new SimpleScriptWrapper(ctx.getLogger());
107+
args.add(AbstractCommandWrapper.resolveFileInPath("graphtyper", null, true).getPath());
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args.add("genotype_sv");
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ReferenceGenome rg = ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id());
111+
if (rg == null)
112+
{
113+
throw new PipelineJobException("Missing reference genome: " + so.getLibrary_id());
114+
}
115+
116+
args.add(rg.getWorkingFastaFile().getPath());
117+
args.add(svVcf.toString());
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119+
args.add("--sam");
120+
args.add(so.getFile().getPath());
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122+
if (threads != null)
123+
{
124+
args.add("--threads");
125+
args.add(threads.toString());
126+
}
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wrapper.execute(args);
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File genotypes = new File(ctx.getWorkingDirectory(), "sv_results/" + SequenceAnalysisService.get().getUnzippedBaseName(so.getName()) + ".vcf.gz");
131+
if (!genotypes.exists())
132+
{
133+
throw new PipelineJobException("Missing file: " + genotypes.getPath());
134+
}
135+
136+
try
137+
{
138+
SequenceAnalysisService.get().ensureVcfIndex(genotypes, ctx.getLogger());
139+
}
140+
catch (IOException e)
141+
{
142+
throw new PipelineJobException(e);
143+
}
144+
145+
ctx.getFileManager().addSequenceOutput(genotypes, "Graphtyper Genotypes: " + so.getName(), "Graphtyper Genoypes", so.getReadset(), null, so.getLibrary_id(), "Input VCF: " + svVcf.getName() + " (" + svVcfId + ")");
146+
}
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}
148+
}
149+
}

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ else if (!svVcf.exists())
115115

116116
if (threads != null)
117117
{
118-
jsonArgs.add("--max_reads");
118+
jsonArgs.add("--cores");
119119
jsonArgs.add(threads.toString());
120120
}
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