Merge pull request #50 from biopet/fix-BIOPET-583

Fixing clever execution

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

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

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -38,17 +38,16 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
   @Input(doc = "Reference")
   var reference: File = _
 
-  protected def cleverOutputDir: File = new File(cleverWorkDir, "work")
   var cleverWorkDir: File = _
 
   @Output(doc = "Clever VCF output")
   lazy val outputvcf: File = {
-    new File(cleverOutputDir, "predictions.vcf")
+    new File(cleverWorkDir, "predictions.vcf")
   }
 
   @Output(doc = "Clever raw output")
   lazy val outputraw: File = {
-    new File(cleverOutputDir, "predictions.raw.txt")
+    new File(cleverWorkDir, "predictions.raw.txt")
   }
 
   //  var T: Option[Int] = config("T", default = defaultThreads)
@@ -60,13 +59,13 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
 
   override def beforeGraph() {
     super.beforeGraph()
-    if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined")
+    if (cleverWorkDir == null) throw new Exception("Clever :: Workdirectory is not defined")
     if (reference == null) reference = referenceFasta()
   }
 
   def cmdLine = required(executable) +
-    " --sorted " +
-    " --use_xa " +
+    required("--sorted") +
+    required("--use_xa") +
     optional("-T", threads) +
     conditional(f, "-f") +
     conditional(a, "-a") +
@@ -74,7 +73,7 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
     conditional(r, "-r") +
     required(input) +
     required(reference) +
-    required(cleverOutputDir)
+    required(cleverWorkDir)
 }
 
 object CleverCaller {

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -23,10 +23,10 @@ class Clever(val parent: Configurable) extends SvCaller {
   def name = "clever"
 
   def biopetScript() {
-    //TODO: check double directories
     for ((sample, bamFile) <- inputBams) {
       val cleverDir = new File(outputDir, sample)
-      val clever = CleverCaller(this, bamFile, cleverDir)
+      val clever = CleverCaller(this, bamFile, new File(cleverDir, "clever_output"))
+      clever.jobOutputFile = new File(cleverDir, ".CleverCaller.out")
       add(clever)
 
       val cleverVCF = new CleverFixVCF(this)