Added main flag to most main jobs

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

@@ -36,7 +36,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   var executable: String = _
 
-  def mainFunction = false
+  var mainFunction = false
 
   /** This is the default shell for drmaa jobs */
   def defaultRemoteCommand = "bash"

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

@@ -85,7 +85,10 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
     this match {
       case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
         logger.info("Write report is skipped because sample flag is used")
-      case _ => reportClass.foreach(add(_))
+      case _ => reportClass.foreach { report =>
+        report.mainFunction = true
+        add(report)
+      }
     }
 
     logger.info("Running pre commands")

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

@@ -14,11 +14,13 @@
  */
 package nl.lumc.sasc.biopet.core
 
-import java.io.{ File, PrintWriter }
+import java.io.{File, PrintWriter}
 
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
-import org.broadinstitute.gatk.queue.function.{ CommandLineFunction, QFunction }
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import org.broadinstitute.gatk.queue.function.{CommandLineFunction, QFunction}
+
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 
@@ -112,6 +114,7 @@ object WriteDependencies extends Logging with Configurable {
           case _                        => None
         }), "main_job" -> (f match {
           case cmd: BiopetCommandLineFunction => cmd.mainFunction
+          case _: WriteSummary                => true
           case _                              => false
         }), "intermediate" -> f.isIntermediate,
           "depends_on_intermediate" -> f.inputs.exists(files(_).isIntermediate),

carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -75,6 +75,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
       samtoolsView.output = preProcessBam.get
       samtoolsView.b = true
       samtoolsView.h = true
+      samtoolsView.mainFunction = true
       add(samtoolsView)
 
       val bamMetricsFilter = BamMetrics(qscript, preProcessBam.get, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
@@ -94,6 +95,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
       macs2.name = Some(sampleId)
       macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
       macs2.fileformat = if (paired) Some("BAMPE") else Some("BAM")
+      macs2.mainFunction = true
       add(macs2)
     }
   }
@@ -131,6 +133,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
         macs2.name = Some(sampleId + "_VS_" + controlId)
         macs2.fileformat = if (paired) Some("BAMPE") else Some("BAM")
         macs2.outputdir = sample.sampleDir + File.separator + "macs2" + File.separator + macs2.name.get + File.separator
+        macs2.mainFunction = true
         add(macs2)
       }
     }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -113,6 +113,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     if (paired) outputFiles += ("fastq_input_R2" -> inputR2.get)
 
     fastqcR1 = Fastqc(this, inputR1, new File(outputDir, R1Name + ".fastqc/"))
+    fastqcR1.mainFunction = true
     add(fastqcR1)
     addSummarizable(fastqcR1, "fastqc_R1")
     outputFiles += ("fastqc_R1" -> fastqcR1.output)
@@ -132,6 +133,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
     if (paired) {
       fastqcR2 = Fastqc(this, inputR2.get, new File(outputDir, R2Name + ".fastqc/"))
+      fastqcR2.mainFunction = true
       add(fastqcR2)
       addSummarizable(fastqcR2, "fastqc_R2")
       outputFiles += ("fastqc_R2" -> fastqcR2.output)
@@ -228,6 +230,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       pipe.deps ::= fastqcR1.output
       pipe.deps ::= fastqcR2.output
       pipe.isIntermediate = !keepQcFastqFiles
+      pipe.mainFunction = true
       add(pipe)
 
       addSummarizable(fqSync, "fastq_sync")

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala

@@ -60,6 +60,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
     flash.fastqR1 = fastqR1
     flash.fastqR2 = fastqR2
     flash.isIntermediate = (forwardPrimers ::: reversePrimers).nonEmpty
+    flash.mainFunction = true
     add(flash)
 
     if ((forwardPrimers ::: reversePrimers).nonEmpty) {
@@ -68,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
       cutadapt.fastqOutput = this.combinedFastq
       cutadapt.statsOutput = swapExt(outputDir, cutadapt.fastqOutput, ".fastq.gz", ".stats")
       (forwardPrimers ::: reversePrimers).foreach(cutadapt.anywhere += _)
+      cutadapt.mainFunction = true
       add(cutadapt)
       addSummarizable(cutadapt, "cutadapt")
     }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala

@@ -56,6 +56,7 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
     if (paired) samtoolsViewSelectUnmapped.f = List("12")
     else samtoolsViewSelectUnmapped.f = List("4")
     samtoolsViewSelectUnmapped.isIntermediate = true
+    samtoolsViewSelectUnmapped.mainFunction = true
     add(samtoolsViewSelectUnmapped)
 
     // start bam to fastq (only on unaligned reads) also extract the matesam
@@ -67,6 +68,7 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
       samToFastq.fastqUnpaired = fastqUnmappedSingletons
     }
     samToFastq.isIntermediate = !config("keep_unmapped_fastq", default = false).asBoolean
+    samToFastq.mainFunction = true
     add(samToFastq)
   }
 }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala

@@ -37,6 +37,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     centrifuge.metFile = Some(centrifugeMetOutput)
     val centrifugeCmd = centrifuge | new Gzip(this) > centrifugeOutput
     centrifugeCmd.threadsCorrection = -1
+    centrifugeCmd.mainFunction = true
     add(centrifugeCmd)
 
     makeKreport("centrifuge", unique = false)
@@ -51,12 +52,15 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     centrifugeKreport.centrifugeOutputFiles :+= fifo
     centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
     centrifugeKreport.onlyUnique = unique
-    add(new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo))))
+    val pipe = new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo))))
+    pipe.mainFunction = true
+    add(pipe)
 
     val krakenReportJSON = new KrakenReportToJson(this)
     krakenReportJSON.inputReport = centrifugeKreport.output
     krakenReportJSON.output = new File(outputDir, s"$outputName.$name.krkn.json")
     krakenReportJSON.skipNames = config("skipNames", default = false)
+    krakenReportJSON.mainFunction = true
     add(krakenReportJSON)
     addSummarizable(krakenReportJSON, s"${name}_report")
   }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala

@@ -52,6 +52,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
     seqtk.output = new File(outputDir, input.getName + ".fasta")
     seqtk.A = true
     seqtk.isIntermediate = true
+    seqtk.mainFunction = true
     add(seqtk)
     seqtk.output
   }
@@ -71,6 +72,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
 
     krakenAnalysis.classifiedOut = Some(new File(outputDir, s"$outputName.krkn.classified.fastq"))
     krakenAnalysis.unclassifiedOut = Some(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
+    krakenAnalysis.mainFunction = true
     add(krakenAnalysis)
 
     outputFiles += ("kraken_output_raw" -> krakenAnalysis.output)
@@ -82,6 +84,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
     krakenReport.input = krakenAnalysis.output
     krakenReport.showZeros = true
     krakenReport.output = new File(outputDir, s"$outputName.krkn.full")
+    krakenReport.mainFunction = true
     add(krakenReport)
 
     outputFiles += ("kraken_report_input" -> krakenReport.input)
@@ -91,6 +94,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
     krakenReportJSON.inputReport = krakenReport.output
     krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
     krakenReportJSON.skipNames = config("skipNames", default = false)
+    krakenReportJSON.mainFunction = true
     add(krakenReportJSON)
     addSummarizable(krakenReportJSON, "krakenreport")
 

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala

@@ -51,11 +51,13 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
     splitLib.input :+= fastqInput
     splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
     sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
+    splitLib.mainFunction = true
     add(splitLib)
 
     val openReference = new PickOpenReferenceOtus(this)
     openReference.inputFasta = addDownsample(splitLib.outputSeqs, new File(splitLib.outputDir, s"${sampleId.get}.downsample.fna"))
     openReference.outputDir = new File(outputDir, "pick_open_reference_otus")
+    openReference.mainFunction = true
     add(openReference)
     _otuMap = openReference.otuMap
     _otuTable = openReference.otuTable

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala

@@ -60,6 +60,7 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     slfR1.input :+= fastqR1
     slfR1.outputDir = new File(outputDir, "split_libraries_fastq_R1")
     sampleId.foreach(slfR1.sampleIds :+= _)
+    slfR1.mainFunction = true
     add(slfR1)
 
     lazy val slfR2 = fastqR2.map { file =>
@@ -74,6 +75,7 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     val pickOtus = new PickOtus(this)
     pickOtus.inputFasta = slfR1.outputSeqs
     pickOtus.outputDir = new File(outputDir, "pick_otus")
+    pickOtus.mainFunction = true
     add(pickOtus)
 
     val pickRepSet = new PickRepSet(this)
@@ -83,6 +85,7 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     pickRepSet.outputFasta = Some(new File(repSetOutputDir, slfR1.outputSeqs.getName))
     pickRepSet.logFile = Some(new File(repSetOutputDir, slfR1.outputSeqs.getName
       .stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna") + ".log"))
+    pickRepSet.mainFunction = true
     add(pickRepSet)
 
     val assignTaxonomy = new AssignTaxonomy(this)
@@ -91,6 +94,7 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     assignTaxonomy.inputFasta = pickRepSet.outputFasta.get
     assignTaxonomy.read1SeqsFp = Some(slfR1.outputSeqs)
     assignTaxonomy.read2SeqsFp = slfR2.map(_.outputSeqs)
+    assignTaxonomy.mainFunction = true
     add(assignTaxonomy)
   }
 }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala

@@ -38,6 +38,7 @@ class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript w
     val seqCount = new SageCountFastq(this)
     seqCount.input = fastqInput
     seqCount.output = countFile
+    seqCount.mainFunction = true
     add(seqCount)
   }
 }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -211,6 +211,7 @@ class Gentrap(val root: Configurable) extends QScript
       ribosomalRefFlat().foreach(job.intervalFile = _)
       job.outputBam = createFile("cleaned.bam")
       job.discardedBam = Some(createFile("rrna.bam"))
+      job.mainFunction = true
       add(job)
       Some(job.outputBam)
     } else bamFile

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala

@@ -35,6 +35,7 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
         baseCounter.outputDir = new File(outputDir, id)
         baseCounter.prefix = id
         baseCounter.refFlat = annotationRefFlat()
+        baseCounter.mainFunction = true
         add(baseCounter)
         id -> baseCounter
     }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala

@@ -33,6 +33,7 @@ trait CufflinksMeasurement extends QScript with Measurement {
     val jobs = bamFiles.map {
       case (id, file) =>
         val cufflinks = makeCufflinksJob(id, file)
+        cufflinks.mainFunction = true
         add(cufflinks)
         id -> cufflinks
     }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala

@@ -41,6 +41,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
           sortSam.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
           sortSam.sortOrder = "queryname"
           sortSam.isIntermediate = true
+          sortSam.mainFunction = true
           add(sortSam)
           sortSam.output
         } else file
@@ -51,6 +52,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
         job.output = new File(outputDir, s"$id.$name.counts")
         job.format = Option("bam")
         job.order = if (sortOnId) Some("name") else Some("pos")
+        job.mainFunction = true
         add(job)
         id -> job
     }

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -200,6 +200,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
     if (chunking) {
       val fastSplitterR1 = new FastqSplitter(this)
+      fastSplitterR1.mainFunction = true
       fastSplitterR1.input = inputR1
       for ((chunkDir, fastqfile) <- chunks) fastSplitterR1.output :+= fastqfile._1
       fastSplitterR1.isIntermediate = true
@@ -207,6 +208,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
       if (paired) {
         val fastSplitterR2 = new FastqSplitter(this)
+        fastSplitterR2.mainFunction = true
         fastSplitterR2.input = inputR2.get
         for ((chunkDir, fastqfile) <- chunks) fastSplitterR2.output :+= fastqfile._2.get
         fastSplitterR2.isIntermediate = true
@@ -255,10 +257,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     if (!skipMarkduplicates) {
       bamFile = new File(outputDir, outputName + ".dedup.bam")
       val md = MarkDuplicates(this, bamFiles, bamFile)
+      md.mainFunction = true
       add(md)
       addSummarizable(md, "mark_duplicates")
     } else if (skipMarkduplicates && chunking) {
       val mergeSamFile = MergeSamFiles(this, bamFiles, new File(outputDir, outputName + ".merge.bam"))
+      mergeSamFile.mainFunction = true
       add(mergeSamFile)
       bamFile = mergeSamFile.output
     }
@@ -297,6 +301,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     bwaAlnR1.fastq = R1
     bwaAlnR1.output = swapExt(output.getParent, output, ".bam", ".R1.sai")
     bwaAlnR1.isIntermediate = true
+    bwaAlnR1.mainFunction = true
     add(bwaAlnR1)
 
     val samFile: File = if (paired) {
@@ -304,6 +309,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       bwaAlnR2.fastq = R2.get
       bwaAlnR2.output = swapExt(output.getParent, output, ".bam", ".R2.sai")
       bwaAlnR2.isIntermediate = true
+      bwaAlnR2.mainFunction = true
       add(bwaAlnR2)
 
       val bwaSampe = new BwaSampe(this)
@@ -314,6 +320,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       bwaSampe.r = getReadGroupBwa
       bwaSampe.output = swapExt(output.getParent, output, ".bam", ".sam")
       bwaSampe.isIntermediate = true
+      bwaSampe.mainFunction = true
       add(bwaSampe)
 
       bwaSampe.output
@@ -324,6 +331,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       bwaSamse.r = getReadGroupBwa
       bwaSamse.output = swapExt(output.getParent, output, ".bam", ".sam")
       bwaSamse.isIntermediate = true
+      bwaSamse.mainFunction = true
       add(bwaSamse)
 
       bwaSamse.output
@@ -331,6 +339,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
     val sortSam = SortSam(this, samFile, output)
     if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+    sortSam.mainFunction = true
     add(sortSam)
     sortSam.output
   }
@@ -346,6 +355,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val pipe = bwaCommand | sortSam
     pipe.isIntermediate = chunking || !skipMarkduplicates
     pipe.threadsCorrection = -1
+    pipe.mainFunction = true
     add(pipe)
     output
   }
@@ -362,6 +372,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
     val pipe = new BiopetFifoPipe(this, gsnapCommand :: ar._1 :: reorderSam :: Nil)
     pipe.threadsCorrection = -2
+    pipe.mainFunction = true
     add(pipe)
     ar._2
   }
@@ -387,6 +398,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val pipe = hisat2 | sortSam
     pipe.isIntermediate = chunking || !skipMarkduplicates
     pipe.threadsCorrection = 1
+    pipe.mainFunction = true
     add(pipe)
 
     output
@@ -402,6 +414,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     tophat.noConvertBam = false
     // and always keep input ordering
     tophat.keepFastaOrder = true
+    tophat.mainFunction = true
     add(tophat)
 
     // fix unmapped file coordinates
@@ -416,6 +429,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val sorter = SortSam(this, fixer.outputSam, new File(tophat.outputDir, "unmapped_fixup.sorted.bam"))
     sorter.sortOrder = "coordinate"
     sorter.isIntermediate = true
+    sorter.mainFunction
     add(sorter)
 
     // merge with mapped file
@@ -456,9 +470,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     stampyCmd.sanger = true
     stampyCmd.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
     stampyCmd.isIntermediate = true
+    stampyCmd.mainFunction = true
     add(stampyCmd)
     val sortSam = SortSam(this, stampyCmd.output, output)
     if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+    sortSam.mainFunction = true
     add(sortSam)
     sortSam.output
   }
@@ -477,6 +493,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val ar = addAddOrReplaceReadGroups(bowtie.output, output)
     val pipe = new BiopetFifoPipe(this, (Some(bowtie) :: Some(ar._1) :: Nil).flatten)
     pipe.threadsCorrection = -1
+    pipe.mainFunction = true
     add(pipe)
     ar._2
   }
@@ -496,6 +513,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val pipe = bowtie2 | sortSam
     pipe.isIntermediate = chunking || !skipMarkduplicates
     pipe.threadsCorrection = -1
+    pipe.mainFunction = true
     add(pipe)
     output
   }
@@ -516,6 +534,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     pipe.threadsCorrection = -3
     zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
     zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
+    pipe.mainFunction = true
     add(pipe)
     reorderSam.output
   }
@@ -528,6 +547,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     zcatR2.foreach(_._1.foreach(add(_)))
 
     val starCommand = Star._2pass(this, zcatR1._2, zcatR2.map(_._2), outputDir, isIntermediate = true)
+    starCommand._2.foreach(_.mainFunction = true)
     addAll(starCommand._2)
     val ar = addAddOrReplaceReadGroups(starCommand._1, output)
     add(ar._1)

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

@@ -217,10 +217,12 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
   def addIndelRealign(inputBam: File, dir: File, isIntermediate: Boolean): File = {
     val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
     realignerTargetCreator.isIntermediate = true
+    realignerTargetCreator.mainFunction = true
     add(realignerTargetCreator)
 
     val indelRealigner = IndelRealigner(this, inputBam, realignerTargetCreator.out, dir)
     indelRealigner.isIntermediate = isIntermediate
+    indelRealigner.mainFunction = true
     add(indelRealigner)
 
     indelRealigner.out
@@ -231,6 +233,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
     val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
 
     if (baseRecalibrator.knownSites.isEmpty) return inputBam
+    baseRecalibrator.mainFunction = true
     add(baseRecalibrator)
 
     if (config("use_analyze_covariates", default = true).asBoolean) {
@@ -244,6 +247,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
     val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
     printReads.BQSR = Some(baseRecalibrator.out)
     printReads.isIntermediate = isIntermediate
+    printReads.mainFunction = true
     add(printReads)
 
     printReads.out

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

@@ -76,6 +76,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
       val mergeSVcalls = new Pysvtools(this)
       mergeSVcalls.input = sampleVCFS.flatten
       mergeSVcalls.output = new File(outputDir, sample + ".merged.vcf")
+      mergeSVcalls.mainFunction = true
       add(mergeSVcalls)
       outputMergedVCFbySample += (sample -> mergeSVcalls.output)
     }
@@ -84,6 +85,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     val mergeSVcallsProject = new Pysvtools(this)
     mergeSVcallsProject.input = outputMergedVCFbySample.values.toList
     mergeSVcallsProject.output = outputMergedVCF
+    mergeSVcallsProject.mainFunction = true
     add(mergeSVcallsProject)
 
     // merging the VCF calls by project
@@ -104,14 +106,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   def summarySettings = Map("sv_callers" -> configCallers.toList)
 
   /** Files for the summary */
-  def summaryFiles: Map[String, File] = {
-    val callers: Set[String] = configCallers
-    //callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
-    Map(
-      "final_mergedvcf" -> outputMergedVCF
-
-    )
-  }
+  def summaryFiles: Map[String, File] = Map("final_mergedvcf" -> outputMergedVCF)
 }
 
 object ShivaSvCalling extends PipelineCommand
\ No newline at end of file

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

@@ -106,22 +106,27 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
       if (normalize && decompose) {
         vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
         vtNormalize.isIntermediate = true
+        vtNormalize.mainFunction = true
         add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
         vtDecompose.inputVcf = vtNormalize.outputVcf
         vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
+        vtDecompose.mainFunction = true
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
         cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
       } else if (normalize && !decompose) {
         vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
+        vtNormalize.mainFunction = true
         add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
         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")
+        vtDecompose.mainFunction = true
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
         cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
       } else cv.variant :+= TaggedFile(caller.outputFile, caller.name)
     }
+    cv.mainFunction = true
     add(cv)
 
     addStats(finalFile, "final")

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala

@@ -30,13 +30,17 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       logger.debug("Starting Breakdancer configuration")
 
       val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
+      bdcfg.mainFunction = true
       val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
+      breakdancer.mainFunction = true
       val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
         sample = sample + sampleNameSuffix)
+      bdvcf.mainFunction = true
 
       val compressedVCF = new SortVcf(this)
       compressedVCF.input = bdvcf.output
       compressedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
+      compressedVCF.mainFunction = true
 
       add(bdcfg, breakdancer, bdvcf, compressedVCF)
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -27,6 +27,7 @@ class Clever(val root: Configurable) extends SvCaller {
     for ((sample, bamFile) <- inputBams) {
       val cleverDir = new File(outputDir, sample)
       val clever = CleverCaller(this, bamFile, cleverDir)
+      clever.mainFunction = true
       add(clever)
 
       val cleverVCF = new CleverFixVCF(this)
@@ -34,11 +35,13 @@ class Clever(val root: Configurable) extends SvCaller {
       cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
       cleverVCF.sampleName = sample + sampleNameSuffix
       cleverVCF.isIntermediate = true
+      cleverVCF.mainFunction = true
       add(cleverVCF)
 
       val compressedVCF = new SortVcf(this)
       compressedVCF.input = cleverVCF.output
       compressedVCF.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
+      compressedVCF.mainFunction = true
       add(compressedVCF)
 
       addVCF(sample, compressedVCF.output)

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

@@ -43,6 +43,7 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "DEL"
         delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
+        delly.mainFunction = true
         add(delly)
 
         catVariants.variant :+= delly.outputvcf
@@ -53,6 +54,7 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "DUP"
         delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
+        delly.mainFunction = true
         add(delly)
 
         catVariants.variant :+= delly.outputvcf
@@ -63,6 +65,7 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "INV"
         delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
+        delly.mainFunction = true
         add(delly)
 
         catVariants.variant :+= delly.outputvcf
@@ -73,6 +76,7 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "TRA"
         delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
+        delly.mainFunction = true
         add(delly)
 
         catVariants.variant :+= delly.outputvcf
@@ -80,11 +84,13 @@ class Delly(val root: Configurable) extends SvCaller {
 
       if (catVariants.variant.isEmpty) Logging.addError("At least 1 SV-type should be selected for Delly")
 
+      catVariants.mainFunction = true
       add(catVariants)
 
       val compressedVCF = new SortVcf(this)
       compressedVCF.input = catVariants.outputFile
       compressedVCF.output = catVariants.outputFile + ".gz"
+      compressedVCF.mainFunction = true
       add(compressedVCF)
 
       addVCF(sample, compressedVCF.output)

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala

@@ -41,9 +41,11 @@ class Pindel(val root: Configurable) extends SvCaller {
       cfg.input = bamFile
       cfg.sampleName = sample + sampleNameSuffix
       cfg.output = configFile
+      cfg.mainFunction = true
       add(cfg)
 
       val pindel = PindelCaller(this, cfg.output, pindelDir)
+      pindel.mainFunction = true
       add(pindel)
 
       // Current date
@@ -56,11 +58,13 @@ class Pindel(val root: Configurable) extends SvCaller {
       pindelVcf.pindelOutputRoot = Some(new File(pindelDir, "sample"))
       pindelVcf.rDate = todayformat.format(today) // officially, we should enter the date of the genome here
       pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
+      pindelVcf.mainFunction = true
       add(pindelVcf)
 
       val compressedVCF = new SortVcf(this)
       compressedVCF.input = pindelVcf.outputVCF
       compressedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
+      compressedVCF.mainFunction = true
       add(compressedVCF)
 
       addVCF(sample, compressedVCF.output)

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

@@ -36,7 +36,9 @@ class Bcftools(val root: Configurable) extends Variantcaller {
     bt.v = true
     bt.c = true
 
-    add(mp | new FixMpileup(this) | bt > outputFile)
+    val pipe = mp | new FixMpileup(this) | bt > outputFile
+    pipe.mainFunction = true
+    add(pipe)
     add(Tabix(this, outputFile))
   }
 }

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

@@ -38,7 +38,9 @@ class BcftoolsSingleSample(val root: Configurable) extends Variantcaller {
       bt.c = true
       bt.output = new File(outputDir, sample + ".vcf.gz")
 
-      add(mp | new FixMpileup(this) | bt)
+      val pipe = mp | new FixMpileup(this) | bt
+      pipe.mainFunction = true
+      add(pipe)
       add(Tabix(this, bt.output))
       bt.output
     }
@@ -48,6 +50,7 @@ class BcftoolsSingleSample(val root: Configurable) extends Variantcaller {
       bcfmerge.input = sampleVcfs