Invert option, true is default now

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

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

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

@@ -88,7 +88,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       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 { report =>
-        report.mainFunction = true
         add(report)
       }
     }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for md5sum */
 class Md5sum(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  mainFunction = false
+
   @Input(doc = "Input")
   var input: File = _
 

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

@@ -30,6 +30,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 class SeqStat(val root: Configurable) extends ToolCommandFunction with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
 
+  mainFunction = false
+
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
   var input: File = null
 

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala

@@ -32,6 +32,8 @@ import scala.io.Source
 class VcfStats(val root: Configurable) extends ToolCommandFunction with Summarizable with Reference {
   def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
 
+  mainFunction = false
+
   @Input(doc = "Input fastq", shortName = "I", required = true)
   var input: File = _
 

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

@@ -75,7 +75,6 @@ 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))
@@ -95,7 +94,6 @@ 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)
     }
   }
@@ -133,7 +131,6 @@ 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

@@ -113,7 +113,6 @@ 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)
@@ -133,7 +132,6 @@ 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)
@@ -230,7 +228,6 @@ 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

@@ -60,7 +60,6 @@ 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) {
@@ -69,7 +68,6 @@ 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

@@ -56,7 +56,6 @@ 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
@@ -68,7 +67,6 @@ 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

@@ -37,7 +37,6 @@ 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)
@@ -53,14 +52,12 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
     centrifugeKreport.onlyUnique = unique
     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

@@ -52,7 +52,6 @@ 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
   }
@@ -72,7 +71,6 @@ 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)
@@ -84,7 +82,6 @@ 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)
@@ -94,7 +91,6 @@ 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

@@ -51,13 +51,11 @@ 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

@@ -60,7 +60,6 @@ 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 =>
@@ -75,7 +74,6 @@ 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)
@@ -85,7 +83,6 @@ 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)
@@ -94,7 +91,6 @@ 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

@@ -38,7 +38,6 @@ 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

@@ -211,7 +211,6 @@ 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

@@ -35,7 +35,6 @@ 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

@@ -33,7 +33,6 @@ 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

@@ -41,7 +41,6 @@ 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
@@ -52,7 +51,6 @@ 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

@@ -200,7 +200,6 @@ 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
@@ -208,7 +207,6 @@ 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
@@ -257,12 +255,10 @@ 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
     }
@@ -301,7 +297,6 @@ 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) {
@@ -309,7 +304,6 @@ 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)
@@ -320,7 +314,6 @@ 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
@@ -331,7 +324,6 @@ 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
@@ -339,7 +331,6 @@ 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
   }
@@ -355,7 +346,6 @@ 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
   }
@@ -372,7 +362,6 @@ 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
   }
@@ -398,7 +387,6 @@ 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
@@ -414,7 +402,6 @@ 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
@@ -429,7 +416,6 @@ 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
@@ -470,11 +456,9 @@ 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
   }
@@ -493,7 +477,6 @@ 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
   }
@@ -513,7 +496,6 @@ 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
   }
@@ -534,7 +516,6 @@ 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
   }
@@ -547,7 +528,6 @@ 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

@@ -217,12 +217,10 @@ 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
@@ -233,7 +231,6 @@ 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) {
@@ -247,7 +244,6 @@ 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