From 5d39aa90b847129fea7be0c92cb6af1a2716382f Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 12 Oct 2016 13:21:28 +0200
Subject: [PATCH] use Option[File] for output dir in stead of String
---
.../lumc/sasc/biopet/extensions/Cnmops.scala | 22 ++++++++++++-------
.../kopisu/methods/CnmopsMethod.scala | 2 +-
2 files changed, 15 insertions(+), 9 deletions(-)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
index 973e65077..619ba7f9d 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
@@ -43,28 +43,34 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction {
// output files, computed automatically from output directory
@Output(doc = "Output CNV file")
lazy val outputCnv: File = {
- require(!outputDir.isEmpty, "Unexpected error when trying to set cn.MOPS CNV output")
- new File(outputDir, "cnv.txt")
+ outputDir match {
+ case Some(dir) if dir.exists => new File(dir, "cnv.txt")
+ case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
+ }
}
@Output(doc = "Output CNR file")
lazy val outputCnr: File = {
- require(!outputDir.isEmpty, "Unexpected error when trying to set cn.MOPS CNR output")
- new File(outputDir, "cnr.txt")
+ outputDir match {
+ case Some(dir) if dir.exists => new File(dir, "cnr.txt")
+ case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
+ }
}
@Output(doc = "Raw output")
lazy val rawOutput: File = {
- require(!outputDir.isEmpty, "Unexpected error when trying to set cn.MOPS raw output")
- new File(outputDir, "rawoutput.txt")
+ outputDir match {
+ case Some(dir) if dir.exists => new File(dir, "rawoutput.txt")
+ case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
+ }
}
/** write all output files to this directory [./] */
- var outputDir: String = _
+ var outputDir: Option[File] = None
override def beforeGraph = {
super.beforeGraph
- require(!outputDir.isEmpty, "Outputdir for cn.MOPS should not be empty")
+ require(outputDir.isDefined, "Outputdir for cn.MOPS should not be empty")
require(input.length >= 2, "Please supply at least 2 BAM files for cn.MOPS")
}
diff --git a/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala b/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
index 3fab95440..d3cf28866 100644
--- a/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
+++ b/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
@@ -27,7 +27,7 @@ class CnmopsMethod(val root: Configurable) extends CnvMethod {
case (sampleName, bamFile) => Some(bamFile)
case _ => None
}.toList
- cnmops.outputDir = new File(outputDir, contig.getSequenceName).getAbsolutePath
+ cnmops.outputDir = Some(new File(outputDir, contig.getSequenceName))
cnmops.beforeGraph
cnmops
}).toList
--
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