From 74d27805bcd27d99d9781dfc5d059d44214f02f0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 27 Jan 2016 11:44:17 +0100
Subject: [PATCH] fixed strandProtocol
---
.../nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 0e7088e6e..455bbd9c9 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -160,7 +160,7 @@ class Gentrap(val root: Configurable) extends QScript
/** Pipeline settings shown in the summary file */
override def summarySettings: Map[String, Any] = super.summarySettings ++ Map(
"expression_measures" -> expMeasures().toList.map(_.toString),
- "strand_protocol" -> strandProtocol.toString,
+ "strand_protocol" -> strandProtocol().toString,
"call_variants" -> shivaVariantcalling.isDefined,
"remove_ribosomal_reads" -> removeRibosomalReads
)
@@ -170,6 +170,9 @@ class Gentrap(val root: Configurable) extends QScript
super.init()
if (expMeasures().isEmpty) Logging.addError("'expression_measures' is missing in the config")
+ require(Gentrap.StrandProtocol.values.contains(strandProtocol()))
+ 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))
}
--
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