From ce85fe0ac30c12fd6a7dc96205de07784d89f34f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 14:10:19 +0200
Subject: [PATCH] Added executable to command
---
.../biopet/extensions/samtools/SamtoolsSort.scala | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
index fee7906d2..cb1f72d8d 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -2,8 +2,9 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
+import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvanthof on 22/09/15.
@@ -19,12 +20,18 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
var compresion: Option[Int] = config("l")
var outputFormat: Option[String] = config("O")
var sortByName: Boolean = config("sort_by_name", default = false)
- val prefix: String = config("prefix", default = new File(qSettings.tempDirectory, output.getAbsolutePath))
+ var prefix: String = _
- def cmdLine = optional("-m", (coreMemeory + "G")) +
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ prefix = config("prefix", default = new File(Files.createTempDir(), output.getAbsolutePath))
+ }
+
+ def cmdLine = executable + required("sort") +
+ optional("-m", (coreMemeory + "G")) +
optional("-@", threads) +
optional("-O", outputFormat) +
conditional(sortByName, "-n") +
- (if (outputAsStsout) "" else required("-o", output)) +
+ (if (outputAsStsout) "" else required("-o", output)) +
(if (inputAsStdin) "" else required(input))
}
--
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