Update on the pipeline, streamline and minimize the required arguments taken from the commandline

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala

@@ -39,30 +39,6 @@ class ConiferAnalyze(val root: Configurable) extends Conifer {
   @Argument(doc = "Minimum population median RPKM per probe", required = false)
   var min_rpkm: Option[Double] = config("min_rpkm")
 
-  override def afterGraph: Unit = {
-    super.afterGraph
-    //
-    //    // create new RPKM_dir with the controls in it together with the subject
-    //    new_rpkm_dir = new File(this.output.getParent() + File.separator + "rpkm_tmp")
-    //    logger.info("Creating " + new_rpkm_dir.getAbsolutePath)
-    //    new_rpkm_dir.mkdir()
-    //
-    //    for (f <- rpkm_dir.listFiles()) {
-    //      var target = new File(new_rpkm_dir + File.separator + f.getName)
-    //      if (!target.exists()) {
-    //        logger.info("Creating " + target.getAbsolutePath)
-    //        Ln(this, f, target, true).run
-    //      }
-    //    }
-    //    for (f <- rpkm_refdir.listFiles()) {
-    //      var target = new File(new_rpkm_dir + File.separator + f.getName)
-    //      if (!target.exists()) {
-    //        logger.info("Creating " + target.getAbsolutePath)
-    //        Ln(this, f, target, true).run
-    //      }
-    //    }
-  }
-
   override def cmdLine = super.cmdLine +
     " analyze " +
     " --probes" + required(probes) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala

@@ -28,10 +28,6 @@ class ConiferCall(val root: Configurable) extends Conifer {
   @Output(doc = "Output calls.txt", shortName = "out")
   var output: File = _
 
-  override def afterGraph {
-    this.checkExecutable
-  }
-
   override def cmdLine = super.cmdLine +
     " call " +
     " --input" + required(input) +

public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala

@@ -84,7 +84,7 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
       var target = new File(RPKMdir + File.separator + f.getName)
       if (!target.exists()) {
         logger.info("Creating " + target.getAbsolutePath)
-        add(Ln(this, f, target, false))
+        add(Ln(this, f, target, true))
         refRPKMlist :+= target
       }
     }
@@ -104,7 +104,7 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
     summary.deps = List(coniferCall.output)
     summary.label = sampleLabel
     summary.calls = coniferCall.output
-    summary.out = input2Calls(inputBam)
+    summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
 
     add(summary)
 

public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala

@@ -26,10 +26,10 @@ import scala.io.Source
 
 class ConiferSummary(val root: Configurable) extends InProcessFunction with Configurable {
   def filterCalls(callFile: File, outFile: File, sampleName: String): Unit = {
-    val filename = callFile.getAbsolutePath
+    //    val filename = callFile.getAbsolutePath
     val writer = new BufferedWriter(new FileWriter(outFile))
 
-    for (line <- Source.fromFile(filename).getLines()) {
+    for (line <- Source.fromFile(callFile).getLines()) {
       line.startsWith(sampleName) || line.startsWith("sampleID") match {
         case true => writer.write(line)
         case _    =>
@@ -58,7 +58,7 @@ class ConiferSummary(val root: Configurable) extends InProcessFunction with Conf
 
   override def run {
     logger.debug("Start")
-    filterCalls(out, calls, label)
+    filterCalls(calls, out, label)
     logger.debug("Stop")
   }
 }