Commit 89bc7d9a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added sunburst plot to mapping and shiva

parent 9ac622a9
......@@ -57,10 +57,10 @@
#{
val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
val bla = ConfigUtils.mapToJson(rawreport)
val jsonReport = ConfigUtils.mapToJson(rawreport)
}#
var krakenresult = JSON.parse('<%= unescape(bla) %>');
var krakenresult = JSON.parse('<%= unescape(jsonReport) %>');
loadGears(krakenresult.kraken.classified);
</script>
......
......@@ -9,8 +9,6 @@ class GearsReport(val root: Configurable) extends ReportBuilderExtension {
object GearsReport extends ReportBuilder {
// FIXME: Not yet finished
// TODO: Sample specific: Add summary (sunflare plot)
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
......
......@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.mapping
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, ReportBuilder }
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
......@@ -33,6 +33,11 @@ object MappingReport extends ReportBuilder {
/** Name of report */
val reportName = "Mapping Report"
override def extFiles = super.extFiles ++ List("js/gears.js")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def krakenExecuted = summary.getValue(sampleId, libId, "gears", "stats", "krakenreport").isDefined
/** Root page for single BamMetrcis report */
def indexPage = {
val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
......@@ -48,7 +53,11 @@ object MappingReport extends ReportBuilder {
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"))) :::
List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
), Map())
), List(
) :::
(if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)), Map()))
else Nil), List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map()
......
......@@ -36,6 +36,9 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
/** Object for report generation for Shiva pipeline */
object ShivaReport extends MultisampleReportBuilder {
override def extFiles = super.extFiles ++ List("js/gears.js")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
/** Root page for the shiva report */
def indexPage = {
val regions = regionsPage
......@@ -136,10 +139,15 @@ object ShivaReport extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
def krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gears", "stats", "krakenreport").isDefined
ReportPage(List(
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
"QC" -> FlexiprepReport.flexiprepPage
), List(
) ::: (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)), Map()))
else Nil), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
......
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