Changeset 5725


Ignore:
Timestamp:
Nov 13, 2019, 1:32:34 PM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1199: Implement Variant calling pipeline

Added RNAseq/Hisat/VariantCall value to the pipeline annotation.

Location:
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java

    r5724 r5725  
    13861386    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
    13871387    Rawdatatype.VARIANT_CALL.addFilter(dc, query);
    1388 //    Pipeline.RNASEQ_HISAT_STRINGTIE.addFilter(dc, query);
     1388    Pipeline.RNASEQ_HISAT_VARIANTCALL.addFilter(dc, query);
    13891389    // The job must be ended
    13901390    query.join(Hql.innerJoin("job", "jb"));
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Pipeline.java

    r5546 r5725  
    4848  public static final Pipeline RNASEQ_HISAT_STRINGTIE = new Pipeline("RNASEQ_HISAT_STRINGTIE", "RNAseq/Hisat/StringTie");
    4949
     50  /**
     51    The new RNAseq alignment and analysis pipeline that uses Hisat and VariantCalling.
     52    @since 4.24
     53  */
     54  public static final Pipeline RNASEQ_HISAT_VARIANTCALL = new Pipeline("RNASEQ_HISAT_VARIANTCALL", "RNAseq/Hisat/VariantCall");
     55 
    5056 
    5157  /**
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

    r5723 r5725  
    3232import net.sf.basedb.core.SessionControl;
    3333import net.sf.basedb.core.Software;
     34import net.sf.basedb.core.StringParameterType;
    3435import net.sf.basedb.opengrid.JobDefinition;
    3536import net.sf.basedb.opengrid.JobStatus;
     
    4849import net.sf.basedb.reggie.dao.Fileserver;
    4950import net.sf.basedb.reggie.dao.Library;
     51import net.sf.basedb.reggie.dao.Pipeline;
    5052import net.sf.basedb.reggie.dao.Rawbioassay;
    5153import net.sf.basedb.reggie.dao.Rawdatatype;
     
    252254      vCallJob.setSendMessage(Values.getBoolean(sc.getUserClientSetting("plugins.sendmessage"), false));
    253255      vCallJob.setName("Run variant calling " + aligned.getName());
     256      vCallJob.setParameterValue("pipeline", new StringParameterType(), Pipeline.RNASEQ_HISAT_VARIANTCALL.getId());
    254257      vCallJob.setParameterValue("alignment", new ItemParameterType<DerivedBioAssay>(DerivedBioAssay.class, null), aligned);
    255258      if (software != null)
     
    269272        String rawName = as.getNextRawBioAssayName(dc, variantCallType);
    270273        RawBioAssay raw = variantCallType.createRawBioAssay(dc);
    271 //        Pipeline.RNASEQ_HISAT_STRINGTIE.setAnnotation(dc, raw);
     274        Pipeline.RNASEQ_HISAT_VARIANTCALL.setAnnotation(dc, raw);
    272275        raw.setJob(vCallJob);
    273276        raw.setName(rawName);
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r5721 r5725  
    495495        jsonChecks.add(checkAnnotationType(dc, Annotationtype.PIPELINE, 1,
    496496            new ValueOptions(Pipeline.RNA_SEQ.getName(), Pipeline.MIPS.getName(),
    497               Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName()),
     497              Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName(),
     498              Pipeline.RNASEQ_HISAT_VARIANTCALL.getName()),
    498499            createIfMissing, effectivePermissionsUse));
    499500       
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