Added snp + indels tree

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -56,13 +56,16 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     add(catConsensusVariantsSnps)
 
     val seed: Int = config("seed", default = 12345)
-    def addRaxml(input: File, outputDir: String, outputName: String) {
+    def addTreeJobs(input: File, outputDir: String, outputName: String) {
+      val dirSufixRaxml = if (outputDir.endsWith(File.separator)) "raxml" else File.separator + "raxml"
+      val dirSufixGubbins = if (outputDir.endsWith(File.separator)) "gubbins" else File.separator + "gubbins"
+
       val raxmlMl = new Raxml(this)
       raxmlMl.input = input
       raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
       raxmlMl.p = seed
       raxmlMl.n = outputName + "_ml"
-      raxmlMl.w = outputDir
+      raxmlMl.w = outputDir + dirSufixRaxml
       raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
       add(raxmlMl)
 
@@ -75,7 +78,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
         raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
         raxmlBoot.p = seed
         raxmlBoot.b = math.abs(r.nextInt)
-        raxmlBoot.w = outputDir
+        raxmlBoot.w = outputDir + dirSufixRaxml
         raxmlBoot.N = 1
         raxmlBoot.n = outputName + "_boot_" + t
         add(raxmlBoot)
@@ -93,17 +96,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       raxmlBi.p = seed
       raxmlBi.f = "b"
       raxmlBi.n = outputName + "_bi"
-      raxmlBi.w = outputDir
+      raxmlBi.w = outputDir + dirSufixRaxml
       add(raxmlBi)
 
       val gubbins = new RunGubbins(this)
       gubbins.fastafile = input
       gubbins.startingTree = raxmlBi.getBipartitionsFile
-      gubbins.outputDirectory = outputDir + "/gubbins/"
+      gubbins.outputDirectory = outputDir + dirSufixGubbins
       add(gubbins)
     }
 
-    addRaxml(catVariantsSnps.output, outputDir + "raxml", "snps")
+    addTreeJobs(catVariantsSnps.output, outputDir + "trees" + File.separator + "snps_only", "snps_only")
+    addTreeJobs(catVariantsSnps.output, outputDir + "trees" + File.separator + "snps_indels", "snps_indels")
   }
 
   // Called for each sample