From 2483b2071c371ada6f22159ba958d75737c1e9a7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 28 Oct 2015 12:34:15 +0100
Subject: [PATCH] Fixed report
---
.../nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp | 2 +-
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala | 7 ++++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
index e442b049e..8c8509346 100644
--- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
@@ -11,7 +11,7 @@
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
<tr>
<th>Variantcallers</th>
- <td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]].mkString(", ")}</td>
+ <td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").getOrElse(List("None")).asInstanceOf[List[String]].mkString(", ")}</td>
</tr>
<tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
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 135b239ad..635e2604f 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
@@ -120,9 +120,10 @@ object ShivaReport 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")),
- "VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
- ), Map())
+ Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))) ++
+ (if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
+ Map("sampleId" -> None))) else Nil)
+ , Map())
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
--
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