Commit 81d36084 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix reference tag

parent 189a25d4
......@@ -32,4 +32,6 @@ object CarpReport extends MultisampleMappingReportTrait {
/** Name of the report */
def reportName = "Carp Report"
override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp")
override def pipelineName = "carp"
}
\ No newline at end of file
......@@ -34,4 +34,6 @@ object GentrapReport extends MultisampleMappingReportTrait {
/** Name of the report */
def reportName = "Gentrap Report"
override def pipelineName = "gentrap"
}
\ No newline at end of file
......@@ -21,20 +21,21 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Front section for the report */
def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp")
def pipelineName = "multisamplemapping"
/** Root page for the carp report */
def indexPage = {
//Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
Map("Reference" -> ReportPage(List(), List(
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> "shiva"))
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
), Map()),
"Files" -> filesPage,
"Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
)), Map())
),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"),
"Report" -> frontSection,
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),
......@@ -57,7 +58,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))), Map())
Map("pipelineName" -> pipelineName, "fileTag" -> "preProcessBam"))), Map())
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
......
......@@ -42,6 +42,8 @@ object ShivaReport extends MultisampleMappingReportTrait {
override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")
override def pipelineName = "shiva"
override def extFiles = super.extFiles ++ List("js/gears.js")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
......
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