From 1db238641aa1385f709c597b382ed327f8994f82 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 9 Feb 2015 15:22:08 +0100
Subject: [PATCH] Fix bug caused by incorrect type usage
---
.../lumc/sasc/biopet/extensions/Fastqc.scala | 24 ++++++++++++++-----
1 file changed, 18 insertions(+), 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 5994d5b66..5d8862e7c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -50,19 +50,31 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
this.checkExecutable
+
+ val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+
contaminants = contaminants match {
+ // user-defined contaminants file take precedence
+ case userDefinedValue @ Some(_) => userDefinedValue
+ // otherwise, use default contaminants file (depending on FastQC version)
case None =>
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
val defaultContams = getVersion match {
- case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/contaminant_list.txt"))
- case _ => Option(new File(fastqcDir + "/Contaminants/contaminant_list.txt"))
+ case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+ case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
}
+ config("contaminants", default = defaultContams)
+ }
+
+ adapters = adapters match {
+ // user-defined contaminants file take precedence
+ case userDefinedValue @ Some(_) => userDefinedValue
+ // otherwise, check if adapters are already present (depending on FastQC version)
+ case None =>
val defaultAdapters = getVersion match {
- case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+ case "v0.11.2" => Some(new File(fastqcDir + "/Configuration/adapter_list.txt"))
case _ => None
}
- config("contaminants", default = defaultContams)
- case wrapped @ Some(_) => wrapped
+ defaultAdapters.collect { case adp => config("adapters", default = adp) }
}
}
--
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