From 3a3027421d7f2ba8b16a79c3a6502829784e6577 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 24 Aug 2016 08:27:09 +0200
Subject: [PATCH] fixing report
---
.../biopet/pipelines/mapping/MultisampleMappingReport.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
index 85709c12c..8d77b9aed 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
@@ -49,7 +49,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
- val pairedFound = summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
+ val mappingExecuted = summary.getLibraryValues("mapping").nonEmpty
+ val pairedFound = !mappingExecuted || summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => value.isDefined }
@@ -72,7 +73,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++
- (if (insertsizeExecuted && pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+ (if (pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
--
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