Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-425

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala

@@ -33,10 +33,15 @@ class SortVcf(val root: Configurable) extends Picard with Reference {
   @Input(doc = "Sequence dictionary to use", required = true)
   var sequenceDictionary: File = _
 
+  @Output
+  private var outputIndex: File = _
+
   override val dictRequired = true
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
+    if (output.getName.endsWith(".vcf.gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+    if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
     if (sequenceDictionary == null) sequenceDictionary = referenceDictFile
   }
 

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

@@ -141,12 +141,20 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
 
     class Library(libId: String) extends AbstractLibrary(libId) {
 
-      lazy val flexiprep = new Flexiprep(qscript)
-      flexiprep.sampleId = Some(sampleId)
-      flexiprep.libId = Some(libId)
-      flexiprep.inputR1 = config("R1")
-      flexiprep.inputR2 = config("R2")
-      flexiprep.outputDir = new File(libDir, "flexiprep")
+      lazy val inputR1: File = config("R1")
+      lazy val inputR2: Option[File] = config("R2")
+
+      lazy val skipFlexiprep: Boolean = config("skip_flexiprep", default = false)
+
+      lazy val flexiprep = if (skipFlexiprep) None else Some(new Flexiprep(qscript))
+      flexiprep.foreach(_.sampleId = Some(sampleId))
+      flexiprep.foreach(_.libId = Some(libId))
+      flexiprep.foreach(_.inputR1 = inputR1)
+      flexiprep.foreach(_.inputR2 = inputR2)
+      flexiprep.foreach(_.outputDir = new File(libDir, "flexiprep"))
+
+      lazy val qcR1: File = flexiprep.map(_.fastqR1Qc).getOrElse(inputR1)
+      lazy val qcR2: Option[File] = flexiprep.map(_.fastqR2Qc).getOrElse(inputR2)
 
       val libraryGears: Boolean = config("library_gears", default = false)
 
@@ -154,17 +162,17 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
 
       /** Function that add library jobs */
       protected def addJobs(): Unit = {
-        inputFiles :+= InputFile(flexiprep.inputR1, config("R1_md5"))
-        flexiprep.inputR2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
-        add(flexiprep)
+        inputFiles :+= InputFile(inputR1, config("R1_md5"))
+        inputR2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+        flexiprep.foreach(add(_))
 
         gearsSingle.foreach { gs =>
           gs.sampleId = Some(sampleId)
           gs.libId = Some(libId)
           gs.outputDir = libDir
 
-          gs.fastqR1 = List(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
-          gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir)).toList
+          gs.fastqR1 = List(addDownsample(qcR1, gs.outputDir))
+          gs.fastqR2 = qcR2.map(addDownsample(_, gs.outputDir)).toList
           add(gs)
         }
       }
@@ -187,11 +195,11 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
       val flexipreps = libraries.values.map(_.flexiprep).toList
 
       val mergeR1: File = new File(sampleDir, s"$sampleId.R1.fq.gz")
-      add(Zcat(qscript, flexipreps.map(_.fastqR1Qc)) | new Gzip(qscript) > mergeR1)
+      add(Zcat(qscript, libraries.values.map(_.qcR1).toList) | new Gzip(qscript) > mergeR1)
 
-      val mergeR2 = if (flexipreps.exists(_.paired)) Some(new File(sampleDir, s"$sampleId.R2.fq.gz")) else None
+      val mergeR2 = if (libraries.values.exists(_.inputR2.isDefined)) Some(new File(sampleDir, s"$sampleId.R2.fq.gz")) else None
       mergeR2.foreach { file =>
-        add(Zcat(qscript, flexipreps.flatMap(_.fastqR2Qc)) | new Gzip(qscript) > file)
+        add(Zcat(qscript, libraries.values.flatMap(_.qcR2).toList) | new Gzip(qscript) > file)
       }
 
       gearsSingle.fastqR1 = List(addDownsample(mergeR1, gearsSingle.outputDir))

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

@@ -46,6 +46,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   def indexPage = {
 
     val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
+    val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
     val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
     val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
@@ -56,9 +57,15 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
     ReportPage(
       List("Samples" -> generateSamplesPage(pageArgs)) ++
-        (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
+        (if (krakenExecuted) List("Dustbin analysis - Kraken" -> ReportPage(List(), List(
           "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), Map()))
+        else Nil) ++ (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_report")
+        )), Map())), List(
+          "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+            Map("summaryStatsTag" -> "centrifuge_unique_report")
+          )), Map("summaryModuleTag" -> "gearscentrifuge")))
         else Nil) ++
         List("Reference" -> ReportPage(List(), List(
           "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
@@ -109,13 +116,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   /** Single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
     val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
+    val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
     val flexiprepExecuted = summary.getLibraryValues("flexiprep")
       .exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
 
     ReportPage(List(
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
-      (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
+      (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+        Map("summaryStatsTag" -> "centrifuge_report")
+      )), Map())), List(
+        "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_unique_report")
+        )), Map("summaryModuleTag" -> "gearscentrifuge")))
+      else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
         "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ++
@@ -133,12 +147,19 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   /** Library page */
   def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
     val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
+    val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
     val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
 
     ReportPage(
       ("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
         (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil) :::
-        (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
+        (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_report")
+        )), Map())), List(
+          "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+            Map("summaryStatsTag" -> "centrifuge_unique_report")
+          )), Map("summaryModuleTag" -> "gearscentrifuge")))
+        else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
           "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), Map()))
         else Nil),