Added report to qiime open reference

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala

@@ -16,9 +16,9 @@ package nl.lumc.sasc.biopet.extensions.qiime
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Created by pjvan_thof on 12/4/15.
@@ -54,7 +54,7 @@ class PickOpenReferenceOtus(val root: Configurable) extends BiopetCommandLineFun
   var minOtuSize: Option[Int] = config("min_otu_size")
   var suppressAlignAndTree: Boolean = config("suppress_taxonomy_assignment", default = false)
 
-  def otuTable = new File(outputDir, "otu_table_mc2.biom")
+  def otuTable = new File(outputDir, "otu_table_mc2_w_tax.biom")
   def failedOtuTable = new File(outputDir, "otu_table_mc2_w_tax_no_pynast_failures.biom")
   def otuMap = new File(outputDir, "final_otu_map.txt")
 

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

@@ -131,8 +131,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     /**
      * Factory method for Library class
-      *
-      * @param id SampleId
+     *
+     * @param id SampleId
      * @return Sample class
      */
     def makeLibrary(id: String): Library = new Library(id)
@@ -224,6 +224,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
 
   /** File to put in the summary for thie pipeline */
   def summaryFiles: Map[String, File] = (
+    qiimeOpenOtuTable.map("qiime_open_otu_table" -> _) ++
+    qiimeOpenOtuMap.map("qiime_open_otu_map" -> _) ++
     qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
     qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
   ).toMap

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

@@ -88,4 +88,3 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
   }
 }
 
-

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

@@ -40,6 +40,9 @@ object GearsReport extends MultisampleReportBuilder {
     val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
     val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path")
       .map(x => new File(x.toString))
+    val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path")
+      .map(x => new File(x.toString))
+
 
     ReportPage(
       (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
@@ -48,6 +51,9 @@ object GearsReport extends MultisampleReportBuilder {
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
         )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+      else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
+        "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
+        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
       else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++
         Map(
           "Versions" -> ReportPage(List(), List(
@@ -71,6 +77,8 @@ object GearsReport extends MultisampleReportBuilder {
     val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
     val qiimeClosesOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
       .map(x => new File(x.toString))
+    val qiimeOpenOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
+      .map(x => new File(x.toString))
 
     ReportPage((if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
       "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
@@ -78,6 +86,9 @@ object GearsReport extends MultisampleReportBuilder {
     else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+    else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
+      "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
+      )), Map("biomFile" -> qiimeOpenOtuTable.get)))
     else Nil) ::: List(
       "Libraries" -> generateLibraryPage(args)
     ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
@@ -91,6 +102,8 @@ object GearsReport extends MultisampleReportBuilder {
     val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
     val qiimeClosesOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
       .map(x => new File(x.toString))
+    val qiimeOpenOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
+      .map(x => new File(x.toString))
 
     ReportPage(
       (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
@@ -100,6 +113,9 @@ object GearsReport extends MultisampleReportBuilder {
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
         )), Map("biomFile" -> qiimeClosesOtuTable.get)))
+      else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> ReportPage(List(), List(
+        "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
+        )), Map("biomFile" -> qiimeOpenOtuTable.get)))
       else Nil), List(
         "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
         "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")