Skip to content

GitLab

Commit e7437482 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added sample and library plots

parent 139202a4
Hide whitespace changes
Inline Side-by-side
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(
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment