From 3921c5d9ab12bd6e6b4995c4a3ebe7b707ac530a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Oct 2015 15:24:19 +0100
Subject: [PATCH] Changed file name
---
.../biopet/pipelines/shiva/ShivaReport.scala | 27 ++++++++++---------
.../biopet/pipelines/shiva/ShivaTrait.scala | 6 ++---
2 files changed, 17 insertions(+), 16 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index b3915dc07..135b239ad 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -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 */
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index c51eb6331..fbfed09cd 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -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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