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Merge pull request #31 from BimberLab/fb_merge_discvr-20.11
Merge discvr-20.11 to discvr-21.3
2 parents 93dc3b0 + a683f0d commit 430c06a

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14 files changed

+147
-19
lines changed

14 files changed

+147
-19
lines changed

‎SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics/.qview.xml‎

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<column name="readset" />
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<column name="analysis_id" />
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<column name="runid" />
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<column name="workbook" />
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</columns>
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<sorts>
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<sort column="dataid/Name"/>

‎SequenceAnalysis/resources/queries/sequenceanalysis/readData/.qview.xml‎

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</properties>
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</column>
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<column name="created" />
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<column name="readset/workbook" />
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<column name="workbook" />
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</columns>
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<sorts>
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<sort column="readset" />

‎SequenceAnalysis/resources/queries/sequenceanalysis/readData/File Details.qview.xml‎

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<column name="archived" />
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<column name="created" />
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<column name="readset/workbook" />
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<column name="workbook" />
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</columns>
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<sorts>
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<sort column="readset" />

‎SequenceAnalysis/resources/queries/sequenceanalysis/readData/With Filepath.qview.xml‎

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<column name="archived" />
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<column name="created" />
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<column name="readset/workbook" />
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<column name="workbook" />
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</columns>
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<sorts>
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<sort column="readset" />

‎SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.327-12.328.sql‎

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ALTER TABLE sequenceanalysis.alignment_summary_junction ADD container ENTITYID;
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UPDATE sequenceanalysis.alignment_summary_junction
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SET container = (SELECT s.container FROM sequenceanalysis.alignment_summary s WHERE s.rowid = alignment_id);

‎SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.327-12.328.sql‎

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ALTER TABLE sequenceanalysis.alignment_summary_junction ADD container ENTITYID;
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GO
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UPDATE sequenceanalysis.alignment_summary_junction
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SET container = (SELECT s.container FROM sequenceanalysis.alignment_summary s WHERE s.rowid = alignment_id);

‎SequenceAnalysis/resources/schemas/sequenceanalysis.xml‎

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</buttonBarOptions>
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</table>
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<table tableName="readData" tableDbType="TABLE" useColumnOrder="true">
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<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
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<javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
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<auditLogging>DETAILED</auditLogging>
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<tableTitle>Sequence Read Data</tableTitle>
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<pkColumnName>rowid</pkColumnName>
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</columns>
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</table>
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<table tableName="quality_metrics" tableDbType="TABLE" useColumnOrder="true">
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<javaCustomizer class="org.labkey.ldk.query.BuiltInColumnsCustomizer" />
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<javaCustomizer class="org.labkey.laboratory.query.LaboratoryTableCustomizer" />
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<auditLogging>DETAILED</auditLogging>
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<tableTitle>Quality Metrics</tableTitle>
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<tableUrl>/query/recordDetails.view?schemaName=sequenceanalysis&amp;query.queryName=Quality_Metrics&amp;keyField=rowid&amp;key=${rowid}</tableUrl>
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<columnTitle>Status</columnTitle>
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<defaultValue>true</defaultValue>
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</column>
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<column columnName="container">
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<isHidden>true</isHidden>
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</column>
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<column columnName="createdby">
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<isHidden>true</isHidden>
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</column>

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

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import org.labkey.sequenceanalysis.run.variant.GenotypeFiltrationStep;
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import org.labkey.sequenceanalysis.run.variant.MendelianViolationReportStep;
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import org.labkey.sequenceanalysis.run.variant.MultiAllelicPositionsHandler;
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import org.labkey.sequenceanalysis.run.variant.PlinkPcaStep;
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import org.labkey.sequenceanalysis.run.variant.SNPEffStep;
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import org.labkey.sequenceanalysis.run.variant.SampleRenameStep;
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import org.labkey.sequenceanalysis.run.variant.SelectSNVsStep;
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@Override
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public Double getSchemaVersion()
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{
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return 12.327;
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return 12.328;
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}
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@Override
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SequencePipelineService.get().registerPipelineStep(new VariantEvalBySampleStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new VariantsToTableStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new VariantQCStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new PlinkPcaStep.Provider());
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SequencePipelineService.get().registerPipelineStep(new MendelianViolationReportStep.Provider());
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//handlers

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java‎

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package org.labkey.sequenceanalysis.run.variant;
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import htsjdk.samtools.util.Interval;
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import org.apache.logging.log4j.Logger;
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import org.json.JSONObject;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
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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.pipeline.VariantProcessingStep;
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import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
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import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
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import javax.annotation.Nullable;
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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.List;
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public class PlinkPcaStep extends AbstractCommandPipelineStep<PlinkPcaStep.PlinkWrapper> implements VariantProcessingStep
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{
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public PlinkPcaStep(PipelineStepProvider provider, PipelineContext ctx)
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{
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super(provider, ctx, new PlinkPcaStep.PlinkWrapper(ctx.getLogger()));
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}
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public static class Provider extends AbstractVariantProcessingStepProvider<PlinkPcaStep>
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{
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public Provider()
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{
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super("PlinkPcaStep", "Plink/PCA", "", "This will run plink to generate the data for MDS/PCA", Arrays.asList(
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ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--not-chr"), "excludedContigs", "Excluded Contigs", "A comma separated list of contigs to exclude, such as X,Y,MT.", "textfield", new JSONObject(){{
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}}, "X,Y,MT")
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), null, "https://zzz.bwh.harvard.edu/plink/");
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}
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public PlinkPcaStep create(PipelineContext ctx)
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{
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return new PlinkPcaStep(this, ctx);
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}
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}
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@Override
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public Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List<Interval> intervals) throws PipelineJobException
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{
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VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
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List<String> args = new ArrayList<>();
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args.add(getWrapper().getExe().getPath());
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args.add("--pca");
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args.add("--allow-extra-chr");
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args.add("--keep WGS.names");
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args.add("--vcf");
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args.add(inputVCF.getPath());
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File outPrefix = new File(outputDirectory, "plink");
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args.add("--out");
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args.add(outPrefix.getPath());
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args.addAll(getClientCommandArgs());
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getWrapper().execute(args);
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output.addInput(inputVCF, "Input VCF");
71+
output.addInput(genome.getWorkingFastaFile(), "Reference Genome");
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File outputFile = new File(outPrefix.getPath() + ".eigenvec");
74+
if (!outputFile.exists())
75+
{
76+
throw new PipelineJobException("Unable to find expected file: " + outputFile);
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}
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output.addOutput(outputFile, "PLink PCA");
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output.addSequenceOutput(outputFile, "PLink PCA for: " + inputVCF.getName(), "PLink PCA", null, null, genome.getGenomeId(), null);
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return output;
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}
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public static class PlinkWrapper extends AbstractCommandWrapper
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{
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public PlinkWrapper(@Nullable Logger logger)
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{
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super(logger);
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}
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public File getExe()
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{
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return SequencePipelineService.get().getExeForPackage("PLINK2PATH", "plink");
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}
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}
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}

‎singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java‎

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multiseq(true),
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htodemux(false),
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dropletutils(true),
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bff(true);
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bff_quantile(true);
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//bff_rec(true);
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boolean isDefault;

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