From 3d73d611581831a9813acb1cd670726a88e2ab2e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 14:06:34 +0100
Subject: [PATCH] Hide QC from report when flexiprep is not executed
---
.../biopet/pipelines/shiva/ShivaReport.scala | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 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 1311c3131..b7b271ca8 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
@@ -143,14 +143,16 @@ object ShivaReport extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
- "QC" -> FlexiprepReport.flexiprepPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
+ val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
+ ReportPage(
+ "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)) ::
+ (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
+ ), "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
+ (if (flexiprepExecuted) List(
+ "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+ )
+ else Nil), args)
}
/** Name of the report */
--
GitLab