Merge pull request #21 from biopet/fix-BIOPET-563

Fixing dependency issue

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala

@@ -41,11 +41,6 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
   @Argument(doc = "What kind of analysis to run: DEL,DUP,INV,TRA")
   var analysistype: String = _
 
-  override def beforeGraph(): Unit = {
-    super.beforeGraph()
-    deps ::= new File(input.getParentFile, input.getName + ".bai")
-  }
-
   def cmdLine = required(executable) +
     "-t" + required(analysistype) +
     "-o" + required(outputvcf) +

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

@@ -62,7 +62,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   var fastqcR1After: Fastqc = _
   var fastqcR2After: Fastqc = _
 
-  override def reportClass = {
+  override def reportClass: Some[FlexiprepReport] = {
     val flexiprepReport = new FlexiprepReport(this)
     flexiprepReport.outputDir = new File(outputDir, "report")
     flexiprepReport.summaryFile = summaryFile
@@ -74,6 +74,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
   /** Function that's need to be executed before the script is accessed */
   def init() {
+    paired = inputR2.isDefined
     if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
     if (sampleId == null || sampleId.isEmpty) Logging.addError("Missing sample ID on flexiprep module")
     if (libId == null || libId.isEmpty) Logging.addError("Missing library ID on flexiprep module")
@@ -147,10 +148,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     }
   }
 
-  def fastqR1Qc = if (paired)
+  def fastqR1Qc: File = if (paired)
     new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.sync.fq.gz")
   else new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.fq.gz")
-  def fastqR2Qc = if (paired)
+  def fastqR2Qc: Option[File] = if (paired)
     Some(new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R2.qc.sync.fq.gz"))
   else None
 
@@ -225,7 +226,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
         /** Must returns stats to store into summary */
         def summaryStats: Any = Map()
 
-        override def summaryDeps = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
+        override def summaryDeps: List[File] = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
       }
 
       pipe.deps ::= fastqcR1.output

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

@@ -84,13 +84,13 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   protected def executeFlexiprep(r1: List[File], r2: List[File]): (File, Option[File]) = {
     val read1: File = if (r1.size == 1) r1.head else {
       val outputFile = new File(outputDir, "merged.R1.fq.gz")
-      Zcat(this, r1) | new Gzip(this) > outputFile
+      add(Zcat(this, r1) | new Gzip(this) > outputFile)
       outputFile
     }
 
     val read2: Option[File] = if (r2.size <= 1) r2.headOption else {
       val outputFile = new File(outputDir, "merged.R2.fq.gz")
-      Zcat(this, r2) | new Gzip(this) > outputFile
+      add(Zcat(this, r2) | new Gzip(this) > outputFile)
       Some(outputFile)
     }
 

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

@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.utils.{ Logging, textToSize }
+import nl.lumc.sasc.biopet.utils.textToSize
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -127,7 +127,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     })
 
   /** Settings to add to summary */
-  def summarySettings = Map(
+  def summarySettings: Map[String, Any] = Map(
     "skip_metrics" -> skipMetrics,
     "skip_flexiprep" -> skipFlexiprep,
     "skip_markduplicates" -> skipMarkduplicates,
@@ -137,7 +137,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     "number_of_chunks" -> (if (chunking) numberChunks.getOrElse(1) else None)
   ) ++ (if (root == null) Map("reference" -> referenceSummary) else Map())
 
-  override def reportClass = {
+  override def reportClass: Some[MappingReport] = {
     val mappingReport = new MappingReport(this)
     mappingReport.outputDir = new File(outputDir, "report")
     mappingReport.summaryFile = summaryFile
@@ -178,6 +178,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
         }
       }
       logger.debug("Chunks: " + numberChunks.getOrElse(1))
+      if (numberChunks.getOrElse(1) <= 1) chunking = false
     }
   }
 
@@ -295,7 +296,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     addSummaryJobs()
   }
 
-  protected lazy val bam2wig = if (config("generate_wig", default = false)) {
+  protected lazy val bam2wig: Option[Bam2Wig] = if (config("generate_wig", default = false)) {
     Some(Bam2Wig(this, finalBamFile))
   } else None
 

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

@@ -67,7 +67,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     Some(report)
   }
 
-  override def defaults: Map[String, Any] = super.defaults ++ Map("reordersam" -> Map("allow_incomplete_dict_concordance" -> true))
+  override def defaults: Map[String, Any] = super.defaults ++ Map(
+    "reordersam" -> Map("allow_incomplete_dict_concordance" -> true),
+    "gears" -> Map("skip_flexiprep" -> true)
+  )
 
   override def fixedValues: Map[String, Any] = super.fixedValues ++ Map("gearssingle" -> Map("skip_flexiprep" -> true))
 
@@ -99,6 +102,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
       lazy val inputR1: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R1"))
       lazy val inputR2: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R2"))
+      lazy val qcFastqR1 = mapping.map(_.flexiprep.fastqR1Qc)
+      lazy val qcFastqR2 = mapping.flatMap(_.flexiprep.fastqR2Qc)
       lazy val inputBam: Option[File] = MultisampleMapping.fileMustBeAbsolute(if (inputR1.isEmpty) config("bam") else None)
       lazy val bamToFastq: Boolean = config("bam_to_fastq", default = false)
       lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
@@ -274,8 +279,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
           add(gears)
         case "all" =>
           val gears = new GearsSingle(qscript)
-          gears.fastqR1 = libraries.flatMap(_._2.inputR1).toList
-          gears.fastqR2 = libraries.flatMap(_._2.inputR2).toList
+          gears.fastqR1 = libraries.flatMap(_._2.qcFastqR1).toList
+          gears.fastqR2 = libraries.flatMap(_._2.qcFastqR2).toList
           gears.sampleId = Some(sampleId)
           gears.outputDir = new File(sampleDir, "gears")
           add(gears)