From db4dcbcabe5b113b4855449ea0b38d63403b8af9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 26 Oct 2015 07:35:41 +0100
Subject: [PATCH] Style changes
---
.../biopet/core/BiopetCommandLineFunction.scala | 13 ++++---------
1 file changed, 4 insertions(+), 9 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index e432c6322..d12675210 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -26,7 +26,6 @@ import org.ggf.drmaa.JobTemplate
import scala.collection.mutable
import scala.io.Source
import scala.sys.process.{ Process, ProcessLogger }
-import scala.util.matching.Regex
import scala.collection.JavaConversions._
/** Biopet command line trait to auto check executable and cluster values */
@@ -50,20 +49,18 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
val writer = new PrintWriter(file)
writer.println("set -eubf")
writer.println("set -o pipefail")
- lines.foreach(writer.println(_))
+ lines.foreach(writer.println)
writer.close()
}
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
- case jt: JobTemplate => {
+ case jt: JobTemplate =>
changeScript(new File(jt.getArgs.head.toString))
jt.setRemoteCommand(remoteCommand)
- }
- case ps: ProcessSettings => {
+ case ps: ProcessSettings =>
changeScript(new File(ps.getCommand.tail.head))
ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
- }
}
/**
@@ -135,10 +132,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
that.beforeGraph()
that.internalBeforeGraph()
this match {
- case p: BiopetPipe => {
+ case p: BiopetPipe =>
p.commands.last._outputAsStdout = true
new BiopetPipe(p.commands ::: that :: Nil)
- }
case _ => new BiopetPipe(List(this, that))
}
}
@@ -209,7 +205,6 @@ object BiopetCommandLineFunction extends Logging {
if (executable != null) {
if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
try {
- val oldExecutable = executable
val buffer = new StringBuffer()
val cmd = Seq("which", executable)
val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
--
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