Changeset 5724


Ignore:
Timestamp:
Nov 13, 2019, 11:09:06 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1199: Implement Variant calling pipeline

Auto-confirmation for the full variant calling should now be implemented. This will behave more like the confirmation for StringTie and Cufflinks which means that we also need a manual confirmation wizard to set the AnalysisResult annotation for the raw bioassays in case there is a problem. The index page has been prepared for this but the wizard is not yet implemented.

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r5685 r5724  
    781781                <span id="mbaf-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
    782782               
    783               <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_start.jsp?ID=<%=ID%>"
    784                 >Start variant calling</span>
    785                 <span class="counter" data-counter="aligned-sequences-for-variant-calling"
    786                   title="Number of aligned sequences waiting for variant calling pipeline">∙</span>
    787                 <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
    788  
    789783              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/stringtie_start.jsp?ID=<%=ID%>"
    790784                >Start StringTie</span>
     
    801795                <span class="counter" data-counter="rawbioassys-without-scanbreport"
    802796                  title="Number of rawbioassays without a SCAN-B report PDF">∙</span>
     797              </ul>
     798            </dd>
     799           
     800            <dt>
     801              <base:icon image="<%=home+"/images/variantcall.png" %>" />
     802              Variant calling pipeline
     803            </dt>
     804           
     805            <dd>
     806              <ul>
     807              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_start.jsp?ID=<%=ID%>"
     808                >Start variant calling</span>
     809                <span class="counter" data-counter="aligned-sequences-for-variant-calling"
     810                  title="Number of aligned sequences waiting for variant calling pipeline">∙</span>
     811                <span id="variant-calling-pipeline-disabled" class="info-warning">auto-processing is disabled</span>
     812              <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/vcall_confirm.jsp?ID=<%=ID%>"
     813                >Confirm variant calling</span>
     814                <span class="counter" data-counter="variantcall-not-confirmed"
     815                  title="Number of VariantCall jobs waiting for confirmation">∙</span>
    803816              </ul>
    804817            </dd>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/AutoConfirmService.java

    r5723 r5724  
    280280        else if (variantCallType.equals(rawType))
    281281        {
    282           //ac = new VariantCallAutoConfirmer(raw);
     282          ac = new VariantCallAutoConfirmer(raw);
    283283        }
    284284     
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/RawOnlyVariantCallAutoConfirmer.java

    r5723 r5724  
    5050 
    5151  /**
    52     Set AutoProcessing to ReProcess on the raw bioassay and remove
     52    Set AutoProcessing to ReProcess on the alignment and remove
    5353    the temporary link to the job.
    5454  */
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java

    r5722 r5724  
    13821382    // ---
    13831383   
     1384    // VariantCall raw bioassays not confirmed
     1385    query = RawBioAssay.getQuery();
     1386    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
     1387    Rawdatatype.VARIANT_CALL.addFilter(dc, query);
     1388//    Pipeline.RNASEQ_HISAT_STRINGTIE.addFilter(dc, query);
     1389    // The job must be ended
     1390    query.join(Hql.innerJoin("job", "jb"));
     1391    query.restrict(Restrictions.neq(Hql.property("jb", "ended"), null));
     1392    // Must NOT have a ANALYSIS_RESULT annotation
     1393    query.join(Annotations.leftJoin(null, Annotationtype.ANALYSIS_RESULT.load(dc), "ar"));
     1394    query.restrict(Restrictions.eq(Hql.alias("ar"), null));
     1395    // Ignore if AutoProcess==AutoConfirm
     1396    query.join(Annotations.leftJoin(null, Annotationtype.AUTO_PROCESSING.load(dc), "ap"));
     1397    query.restrict(
     1398        Restrictions.or(
     1399          Restrictions.neq(Hql.alias("ap"), Expressions.string("AutoConfirm")),
     1400          Restrictions.eq(Hql.alias("ap"), null)
     1401        ));
     1402    query.setCacheResult(true);
     1403    json.put("variantcall-not-confirmed", query.count(dc));
     1404    // ---
     1405
     1406   
    13841407    // Items marked for removal
    13851408    query = RawBioAssay.getQuery();
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