Commit d19d4308 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-merge_issues' into 'develop'

Fix merge issues



See merge request !321
parents 75cd9a9b 088aa902
......@@ -7,9 +7,9 @@ class LazyCheck[T](function: => T) {
private var _isSet = false
def isSet = _isSet
lazy val value = {
val chache = function
val cache = function
_isSet = true
chache
cache
}
def apply() = value
def get = value
......
......@@ -177,7 +177,7 @@ class Gentrap(val root: Configurable) extends QScript
if (removeRibosomalReads && ribosomalRefFlat().isEmpty)
Logging.addError("removeRibosomalReads is enabled but no ribosomalRefFlat is given")
executedMeasures.foreach(x => x.outputDir = new File(outputDir, "expresion_measures" + File.separator + x.name))
executedMeasures.foreach(x => x.outputDir = new File(outputDir, "expression_measures" + File.separator + x.name))
}
/** Pipeline run for multiple samples */
......@@ -208,8 +208,8 @@ class Gentrap(val root: Configurable) extends QScript
val job = new WipeReads(qscript)
job.inputBam = bamFile.get
ribosomalRefFlat().foreach(job.intervalFile = _)
job.outputBam = createFile(".cleaned.bam")
job.discardedBam = createFile(".rrna.bam")
job.outputBam = createFile("cleaned.bam")
job.discardedBam = createFile("rrna.bam")
add(job)
Some(job.outputBam)
} else bamFile
......
......@@ -21,6 +21,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Front section for the report */
def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp")
def additionalSections: List[(String, ReportSection)] = Nil
def pipelineName = "multisamplemapping"
/** Root page for the carp report */
......@@ -42,8 +44,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)), Map())
),
List(
"Report" -> frontSection,
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
"Report" -> frontSection) ++
additionalSections ++
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++
(if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
......
......@@ -47,16 +47,16 @@ object ShivaReport extends MultisampleMappingReportTrait {
override def extFiles = super.extFiles ++ List("js/gears.js")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
override def additionalSections = super.additionalSections ++ (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
Map("showPlot" -> true, "showTable" -> false)))
else Nil)
/** Root page for the shiva report */
override def indexPage = {
val variantcallingSection = (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
Map("showPlot" -> true, "showTable" -> false)))
else Nil)
val regions = regionsPage
val oldPage = super.indexPage
oldPage.copy(sections = oldPage.sections.head :: variantcallingSection ::: oldPage.sections.tail, subPages = oldPage.subPages ++ regionsPage)
oldPage.copy(subPages = oldPage.subPages ++ regionsPage)
}
/** Generate a page with all target coverage stats */
......
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