Commit cf8259b9 authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

Removed some variables from ssp file.

parent e859f656
......@@ -33,6 +33,8 @@
<%@ var librariesCount: Int %>
<%@ var clipCount: Int %>
<%@ var trimCount: Int %>
<%@ var flexiprepReportPlotRead1: Option[Unit] %>
<%@ var flexiprepReportPlotRead2: Option[Unit] %>
<%@ var %>
#if (showIntro)
......@@ -76,8 +78,8 @@
#if (showPlot)
#{
FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
if (paired) FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
flexiprepReportPlotRead1.getOrElse(None)
if (paired) flexiprepReportPlotRead2.getOrElse(None)
}#
<div class="panel-body">
<div class="row">
......
......@@ -296,11 +296,13 @@ object FlexiprepReadSummary {
object FlexiprepReadSummaryReportPage {
def values(summary: SummaryDb,
outputDir: File,
runId: Int,
allSamples: Seq[Sample],
allLibraries: Seq[Library],
sampleId: Option[Int] = None,
libId: Option[Int] = None) = {
libId: Option[Int] = None,
showPlot: Boolean = false )= {
val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map("skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
......@@ -314,11 +316,23 @@ object FlexiprepReadSummaryReportPage {
val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
val librariesCount = libraries.size
/* Todo: Map this conditionally */
if (showPlot){
val flexiprepReportPlotRead1: Option[Unit] = Some(FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId))
if (paired) {
val flexiprepReportPlotRead2: Option[Unit] = Some(FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId))
else val flexiprepReportPlotRead2: Option[Unit] = None
else val flexiprepReportPlotRead1: Option[Unit] = None
}
}
Map(
"summary" -> summary,
"outputDir" -> outputDir,
"runId" -> runId,
"sampleId" -> sampleId,
"libId" -> libId,
"showPlot"
"settings" -> settings,
"samples" -> samples,
"libraries" -> libraries,
......@@ -327,13 +341,7 @@ object FlexiprepReadSummaryReportPage {
"librariesCount" -> librariesCount
)
}
def settings(summary: SummaryDb,
runId: Int) = { }
def paired(summary: SummaryDb,
runId: Int,
sampleId: Option[Int],
libId: Option[Int]) =
}
Supports Markdown
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