Commit d04e8e50 authored by rhpvorderman's avatar rhpvorderman

Added krakenkronaplot.values to all calls of krakenkrona.ssp

parent 4b3cb306
......@@ -104,12 +104,22 @@ object GearsReport extends MultisampleReportBuilder {
val krakenPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(
ReportPage(List(),
List("Krona plot" -> Future.successful(
ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)))),
Map())))
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> Future.successful(
ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId)))),
Map()
)))
else None
val qiimeClosedPage =
......@@ -183,21 +193,22 @@ object GearsReport extends MultisampleReportBuilder {
val gearsCentrifugePage = if (centrifugeExecuted) {
Some(
"Centrifuge analysis" -> Future.successful(ReportPage(
List(
"Non-unique" -> Future.successful(
ReportPage(List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
SampleId,
libId,
Some("centrifuge")))),
Map()))),
List("Non-unique" -> Future.successful(ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
SampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
......@@ -208,12 +219,21 @@ object GearsReport extends MultisampleReportBuilder {
val krakenAnalysisPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(
ReportPage(List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId))),
Map())))
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId))),
Map()
)))
else None
val qiimeClosesOtuTablePage =
......@@ -295,21 +315,22 @@ object GearsReport extends MultisampleReportBuilder {
if (centrifugeExecuted)
Some(
"Centrifuge analysis" -> Future.successful(ReportPage(
List(
"Non-unique" -> Future.successful(
ReportPage(List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
SampleId,
libId,
Some("centrifuge")))),
Map()))),
List("Non-unique" -> Future.successful(ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
SampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
......@@ -320,12 +341,21 @@ object GearsReport extends MultisampleReportBuilder {
val krakenAnalysisPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(
ReportPage(List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId))),
Map())))
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId))),
Map()
)))
else None
val qiimeClosesOtuTablePage =
......
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