Adding more output files to gearssingle

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

@@ -85,8 +85,8 @@ object GearsReport extends MultisampleReportBuilder {
   def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
     val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", sample = sampleId, library = NoLibrary), Duration.Inf) == 1
     val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId, library = None), Duration.Inf) == 1
-    val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf)
-    val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gears", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf)
+    val qiimeClosesOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_closed_otu_table"), Duration.Inf)
+    val qiimeOpenOtuTable = Await.result(summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), Duration.Inf)
 
     ReportPage((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")

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

@@ -150,6 +150,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
       centrifuge.fastqR2 = r2
       centrifuge.outputName = outputName
       add(centrifuge)
+      outputFiles += "centrifuge_output" -> centrifuge.centrifugeOutput
     }
 
     qiimeRatx foreach { qiimeRatx =>
@@ -163,18 +164,21 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
       qiimeClosed.outputDir = new File(outputDir, "qiime_closed")
       qiimeClosed.fastqInput = combinedFastq
       add(qiimeClosed)
+      outputFiles += "qiime_closed_otu_table" -> qiimeClosed.otuTable
     }
 
     qiimeOpen foreach { qiimeOpen =>
       qiimeOpen.outputDir = new File(outputDir, "qiime_open")
       qiimeOpen.fastqInput = combinedFastq
       add(qiimeOpen)
+      outputFiles += "qiime_open_otu_table" -> qiimeOpen.otuTable
     }
 
     seqCount.foreach { seqCount =>
       seqCount.fastqInput = combinedFastq
       seqCount.outputDir = new File(outputDir, "seq_count")
       add(seqCount)
+      outputFiles += "seq_count_count_file" -> seqCount.countFile
     }
 
     addSummaryJobs()