Changeset 5725

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:

• counter/CounterService.java (modified) (1 diff)
• dao/Pipeline.java (modified) (1 diff)
• grid/VariantCallingJobCreator.java (modified) (4 diffs)
• servlet/InstallServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/counter/CounterService.java

@@ -1386 +1386 @@
     query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
     Rawdatatype.VARIANT_CALL.addFilter(dc, query);
-//    Pipeline.RNASEQ_HISAT_STRINGTIE.addFilter(dc, query);
+    Pipeline.RNASEQ_HISAT_VARIANTCALL.addFilter(dc, query);
     // The job must be ended
     query.join(Hql.innerJoin("job", "jb"));

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Pipeline.java

@@ -48 +48 @@
   public static final Pipeline RNASEQ_HISAT_STRINGTIE = new Pipeline("RNASEQ_HISAT_STRINGTIE", "RNAseq/Hisat/StringTie");
 
+  /**
+    The new RNAseq alignment and analysis pipeline that uses Hisat and VariantCalling.
+    @since 4.24
+  */
+  public static final Pipeline RNASEQ_HISAT_VARIANTCALL = new Pipeline("RNASEQ_HISAT_VARIANTCALL", "RNAseq/Hisat/VariantCall");
+  
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

@@ -32 +32 @@
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Software;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.opengrid.JobDefinition;
 import net.sf.basedb.opengrid.JobStatus;
@@ -48 +49 @@
 import net.sf.basedb.reggie.dao.Fileserver;
 import net.sf.basedb.reggie.dao.Library;
+import net.sf.basedb.reggie.dao.Pipeline;
 import net.sf.basedb.reggie.dao.Rawbioassay;
 import net.sf.basedb.reggie.dao.Rawdatatype;
@@ -252 +254 @@
       vCallJob.setSendMessage(Values.getBoolean(sc.getUserClientSetting("plugins.sendmessage"), false));
       vCallJob.setName("Run variant calling " + aligned.getName());
+      vCallJob.setParameterValue("pipeline", new StringParameterType(), Pipeline.RNASEQ_HISAT_VARIANTCALL.getId());
       vCallJob.setParameterValue("alignment", new ItemParameterType<DerivedBioAssay>(DerivedBioAssay.class, null), aligned);
       if (software != null) 
@@ -269 +272 @@
         String rawName = as.getNextRawBioAssayName(dc, variantCallType);
         RawBioAssay raw = variantCallType.createRawBioAssay(dc);
-//        Pipeline.RNASEQ_HISAT_STRINGTIE.setAnnotation(dc, raw);
+        Pipeline.RNASEQ_HISAT_VARIANTCALL.setAnnotation(dc, raw);
         raw.setJob(vCallJob);
         raw.setName(rawName);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -495 +495 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.PIPELINE, 1, 
             new ValueOptions(Pipeline.RNA_SEQ.getName(), Pipeline.MIPS.getName(), 
-              Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName()), 
+              Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName(),
+              Pipeline.RNASEQ_HISAT_VARIANTCALL.getName()), 
             createIfMissing, effectivePermissionsUse));