Commit 6173485e authored by Wai Yi Leung's avatar Wai Yi Leung

Use samplename_suffix to change the sample name

parent ef811002
......@@ -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
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
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