Commit 5b90369c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Removing the cd commands inside the job

parent 3019cf79
......@@ -54,7 +54,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
writer.println("set -eubf")
writer.println("set -o pipefail")
lines.foreach(writer.println)
//lines.foreach(writer.println)
writer.println(this.commandLine)
jobDelayTime.foreach(x => writer.println(s"sleep $x"))
writer.close()
}
......@@ -99,6 +100,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph()
internalBeforeGraph()
this.commandDirectory = this.jobOutputFile.getParentFile
super.freezeFieldValues()
}
......
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