From 1a5a202c2ddea086545e2a2bcc3c01684c99b17c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Aug 2015 13:35:41 +0200
Subject: [PATCH] Changes ; to &&, is saver
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 8a4980342..ab60204ac 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -87,7 +87,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
/** Returns command to execute */
def cmdLine = {
- var cmd: String = required("cd", outputDir) + "&&" + required(executable)
+ var cmd: String = required("cd", outputDir) + " && " + required(executable)
if (runmode != null && runmode == "genomeGenerate") { // Create index
cmd += required("--runMode", runmode) +
required("--genomeFastaFiles", reference)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
index f787ccab9..f07f18a1e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
@@ -30,7 +30,7 @@ class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction {
outputFiles ::= new File(reference.getParentFile, baseName + ".2.bt2")
}
- def cmdLine = required("cd", reference.getParentFile) + "; " +
+ def cmdLine = required("cd", reference.getParentFile) + " && " +
required(executable) +
required(reference) +
required(baseName)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
index f9611fa5c..ad8cbec14 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
@@ -30,7 +30,7 @@ class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction {
outputFiles ::= new File(reference.getParentFile, baseName + ".2.ebwt")
}
- def cmdLine = required("cd", reference.getParentFile) + "; " +
+ def cmdLine = required("cd", reference.getParentFile) + " && " +
required(executable) +
required(reference) +
required(baseName)
--
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