Commit 9605d702 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix camelCase names

parent db06f6bc
......@@ -14,10 +14,10 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
@Input(doc = "Input file (bam)")
var input: File = _
var workdir: File = _
var workDir: File = _
@Output(doc = "Delly result VCF")
var outputvcf: File = _
var outputVcf: File = _
var outputBaseName: File = _
......@@ -36,8 +36,8 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
var outputFiles: Map[String, File] = Map()
var vcfFiles: Map[String, File] = Map()
this.outputBaseName = workdir + input.getName.substring(0, input.getName.lastIndexOf(".bam"))
this.outputvcf = outputBaseName + ".delly.vcf"
this.outputBaseName = workDir + input.getName.substring(0, input.getName.lastIndexOf(".bam"))
this.outputVcf = outputBaseName + ".delly.vcf"
/// start delly and then copy the vcf into the root directory "<sample>.delly/"
if (del) {
......@@ -79,14 +79,14 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
//TODO: convert to biopet extension
val variants = new CatVariants()
variants.variant = vcfFiles.values.toList
variants.outputFile = this.outputvcf
variants.outputFile = this.outputVcf
variants.reference = referenceFasta()
// add the job
add(variants)
Some(outputvcf)
Some(outputVcf)
} else if (vcfFiles.size == 1) {
// TODO: pretify this
val ln = Ln(this, vcfFiles.head._2, this.outputvcf, relative = true)
val ln = Ln(this, vcfFiles.head._2, this.outputVcf, relative = true)
add(ln)
Some(ln.output)
} else None
......@@ -101,7 +101,7 @@ object Delly extends PipelineCommand {
def apply(root: Configurable, input: File, runDir: File): Delly = {
val dellyPipeline = new Delly(root)
dellyPipeline.input = input
dellyPipeline.workdir = runDir
dellyPipeline.workDir = runDir
dellyPipeline.init()
dellyPipeline.biopetScript()
dellyPipeline
......
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