Merge branch 'develop' into fix-BIOPET-563

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -107,6 +107,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       count += 1
       if (count % 500 == 0) logger.info(s"Preprocessing done for ${count} jobs out of ${functions.length} total")
     }
+    logger.info(s"Preprocessing done for ${functions.length} functions")
 
     val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
 
@@ -121,6 +122,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
     }
 
+    logger.info("Set stdout file when not set")
     functions.filter(_.jobOutputFile == null).foreach(f => {
       val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
       BiopetQScript.safeOutputs(f) match {
@@ -132,6 +134,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     if (!skipWriteDependencies) WriteDependencies.writeDependencies(
       functions,
       new File(logDir, "graph"))
+    else logger.debug("Write dependencies is skipped")
 
     Logging.checkErrors()
     logger.info("Script complete without errors")

docs/pipelines/shiva.md

@@ -196,6 +196,8 @@ variantcallers:
     - haplotypecaller
     - unifiedgenotyper
     - haplotypecaller_gvcf
+unifiedgenotyper:
+    merge_vcf_results: false # This will do the variantcalling but will not merged into the final vcf file
 ```
 
 **Additional XHMM CNV calling example**

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -84,6 +84,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
   def biopetScript(): Unit = {
     require(inputBams.nonEmpty, "No input bams found")
     require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + ShivaVariantcalling.callersList(this).map(_.name).mkString(", "))
+    if (!callers.exists(_.mergeVcfResults)) Logging.addError("must select at least 1 variantcaller where merge_vcf_results is true")
 
     addAll(dbsnpVcfFile.map(Shiva.makeValidateVcfJobs(this, _, referenceFasta(), new File(outputDir, ".validate"))).getOrElse(Nil))
 
@@ -91,7 +92,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
     cv.out = finalFile
     cv.setKey = Some("VariantCaller")
     cv.genotypemergeoption = Some("PRIORITIZE")
-    cv.rod_priority_list = Some(callers.map(_.name).mkString(","))
+    cv.rod_priority_list = Some(callers.filter(_.mergeVcfResults).map(_.name).mkString(","))
     for (caller <- callers) {
       caller.inputBams = inputBams
       caller.namePrefix = namePrefix
@@ -112,21 +113,22 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
         vtDecompose.inputVcf = vtNormalize.outputVcf
         vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
-        cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
       } else if (normalize && !decompose) {
         vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
         add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
-        cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
       } else if (!normalize && decompose) {
         vtDecompose.inputVcf = caller.outputFile
         vtDecompose.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".decompose.vcf.gz")
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
-        cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
-      } else cv.variant :+= TaggedFile(caller.outputFile, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
+      } else if (caller.mergeVcfResults) cv.variant :+= TaggedFile(caller.outputFile, caller.name)
+    }
+    if (cv.variant.nonEmpty) {
+      add(cv)
+      addStats(finalFile, "final")
     }
-    add(cv)
-
-    addStats(finalFile, "final")
 
     addSummaryJobs()
   }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala

@@ -27,6 +27,8 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
 
   var namePrefix: String = _
 
+  val mergeVcfResults: Boolean = config("merge_vcf_results", default = true)
+
   /**
    * Map of samplename -> (preprocessed) bam file
    */