Fix output dirs and set default single sample calling off

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

@@ -25,7 +25,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     "ploidy" -> 1,
     "use_haplotypecaller" -> false,
     "use_unifiedgenotyper" -> true,
-    "joint_variantcalling" -> true
+    "joint_variantcalling" -> true,
+    "single_sample_calling" -> false
   ), super.defaults)
 
   var gatkPipeline: GatkPipeline = new GatkPipeline(qscript)
@@ -60,8 +61,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 
   def addMultiSampleJobs(): Unit = {
-    val refVariants = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference")
-    val refVariantSnps = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference", snpsOnly = true)
+    val refVariants = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference")
+    val refVariantSnps = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference", snpsOnly = true)
 
     val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList,
       new File(outputDir, "fastas" + File.separator + "variant.fasta"))
@@ -94,7 +95,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
       raxmlMl.p = seed
       raxmlMl.n = outputName + "_ml"
-      raxmlMl.w = outputDir + dirSufixRaxml
+      raxmlMl.w = dirSufixRaxml
       raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
       add(raxmlMl)
 
@@ -114,7 +115,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
         raxmlBoot.getBootstrapFile
       }
 
-      val cat = Cat(this, bootList.toList, outputDir + "/boot_list")
+      val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
       add(cat)
 
       val raxmlBi = new Raxml(this)
@@ -125,7 +126,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       raxmlBi.p = seed
       raxmlBi.f = "b"
       raxmlBi.n = outputName + "_bi"
-      raxmlBi.w = outputDir + dirSufixRaxml
+      raxmlBi.w = dirSufixRaxml
       add(raxmlBi)
 
       val gubbins = new RunGubbins(this)
@@ -150,9 +151,9 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     if (gatkPipeline.samples.contains(sampleName)) {
       bastyGenerateFasta.bamFile = gatkPipeline.samples(sampleName).gatkVariantcalling.scriptOutput.bamFiles.head
     }
-    bastyGenerateFasta.outputVariants = outputDir + bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
-    bastyGenerateFasta.outputConsensus = outputDir + bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
-    bastyGenerateFasta.outputConsensusVariants = outputDir + bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
+    bastyGenerateFasta.outputVariants = new File(outputDir, bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+    bastyGenerateFasta.outputConsensus = new File(outputDir, bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+    bastyGenerateFasta.outputConsensusVariants = new File(outputDir, bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
     bastyGenerateFasta.sampleName = sampleName
     bastyGenerateFasta.snpsOnly = snpsOnly
     qscript.add(bastyGenerateFasta)