Use samplename_suffix to change the sample name

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

@@ -33,7 +33,7 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
       val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
       val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
-        sample = sample + "_bd")
+        sample = sample + sampleNameSuffix)
 
       val compressedVCF = new SortVcf(this)
       compressedVCF.input = bdvcf.output

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

@@ -33,7 +33,7 @@ class Clever(val root: Configurable) extends SvCaller {
       val cleverVCF = new CleverFixVCF(this)
       cleverVCF.input = clever.outputvcf
       cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
-      cleverVCF.sampleName = sample + "_cl"
+      cleverVCF.sampleName = sample + sampleNameSuffix
       cleverVCF.isIntermediate = true
       add(cleverVCF)
 

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

@@ -40,7 +40,7 @@ class Pindel(val root: Configurable) extends SvCaller {
       val configFile: File = new File(pindelDir, sample + ".pindel.cfg")
       val cfg = new PindelConfig(this)
       cfg.input = bamFile
-      cfg.sampleName = sample + "_pd" // pindel suffix
+      cfg.sampleName = sample + sampleNameSuffix
       cfg.output = configFile
       add(cfg)
 

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

@@ -30,6 +30,8 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
 
   var inputBams: Map[String, File] = Map.empty
 
+  val sampleNameSuffix: String = config("samplename_suffix", default="")
+
   def outputVCF(sample: String): Option[File] = {
     outputVCFs.get(sample) match {
       case Some(file) => Some(file)