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biopet.biopet
Commit e7437482 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added sample and library plots

parent 139202a4
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Showing with 16 additions and 2 deletions
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ e7437482
......@@ -81,12 +81,19 @@ object GearsReport 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 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(
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")
)), 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("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
......@@ -106,6 +113,7 @@ object GearsReport extends MultisampleReportBuilder {
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
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 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")
......@@ -113,7 +121,13 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
) ::: (if (krakenExecuted) List("Kraken" -> 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("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
......
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