Commit 3921c5d9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed file name

parent 85735dd3
......@@ -38,7 +38,7 @@ object ShivaReport extends MultisampleReportBuilder {
def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match {
case Some(true) => true
case _ => false
case _ => false
}
/** Root page for the shiva report */
......@@ -58,19 +58,20 @@ object ShivaReport extends MultisampleReportBuilder {
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")) ++
(if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
Map("showPlot" -> true, "showTable" -> false))) else Nil) ++
Map("showPlot" -> true, "showTable" -> false)))
else Nil) ++
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
),
pageArgs
)
}
......@@ -135,8 +136,8 @@ object ShivaReport extends MultisampleReportBuilder {
"Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true))) ++
(if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil) ++
List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args)
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args)
}
/** Library page */
......
......@@ -121,7 +121,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
lazy val inputR1: Option[File] = config("R1")
lazy val inputR2: Option[File] = config("R2")
lazy val inputBam: Option[File] = if (r1.isEmpty) config("bam") else None
lazy val inputBam: Option[File] = if (inputR1.isEmpty) config("bam") else None
lazy val (mapping, bamFile, preProcessBam): (Option[Mapping], Option[File], Option[File]) =
(inputR1.isDefined, inputBam.isDefined) match {
......@@ -226,9 +226,9 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input == Nil) None
else if (input.tail == Nil) {
val bamFile = new File(sampleDir, input.head.getName)
val bamFile = new File(sampleDir, s"$sampleId.bam")
val oldIndex: File = new File(input.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
val newIndex: File = new File(sampleDir, input.head.getName.stripSuffix(".bam") + ".bai")
val newIndex: File = new File(sampleDir, s"$sampleId.bai")
val baiLn = Ln(qscript, oldIndex, newIndex)
add(baiLn)
......
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