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biopet.biopet
Commits
36f14bb5
Commit
36f14bb5
authored
Sep 20, 2016
by
Peter van 't Hof
Browse files
Fixed report
parent
96137126
Changes
2
Hide whitespace changes
Inline
Side-by-side
gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
View file @
36f14bb5
...
...
@@ -10,12 +10,13 @@
<%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
<%@ var summaryTag: String = "krakenreport" %>
<%@ var summaryStatsTag: String = "krakenreport" %>
<%@ var summaryModuleTag: String = "gearskraken" %>
<%
val summaries = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues(
"gearskraken"
, "stats", summaryTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId,
"gearskraken"
, "stats", summaryTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
summary.getSampleValues(
summaryModuleTag
, "stats", summary
Stats
Tag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId,
summaryModuleTag
, "stats", summary
Stats
Tag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
36f14bb5
...
...
@@ -47,7 +47,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage
(
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
(
"summaryTag"
->
"centri
g
uge_report"
)))
)),
Map
(
"summary
Stats
Tag"
->
"centri
f
uge_report"
,
"summaryModuleTag"
->
"gearscentrifuge"
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
...
...
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