Commit 3ce114fa authored by Sander Bollen's avatar Sander Bollen
Browse files

fix several issues

parent 824daf88
......@@ -16,40 +16,44 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
This tool creates several files with `out` as the root
*/
@Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written")
var out: String = _
lazy val outFile: File = {
new File(out)
}
var out: File = _
@Output
lazy val summaryFile: File = {
new File(out + "_summary")
}
@Output
lazy val statisticsFile: File = {
new File(out + "_statistics")
}
@Output
lazy val intervalSummaryFile: File = {
new File(out + "_interval_summary")
}
@Output
lazy val intervalStatisticsFile: File = {
new File(out + "_interval_statistics")
}
@Output
lazy val geneSummaryFile: File = {
new File(out + "_gene_summary")
}
@Output
lazy val geneStatisticsFile: File = {
new File(out + "_gene_statistics")
}
@Output
lazy val cumulativeCoverageCountsFile: File = {
new File(out + "_cumulative_coverage_counts")
}
@Output
lazy val cumulativeCoverageProportionsFile: File = {
new File(out + "_cumulative_coverage_proportions")
}
......
......@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version {
executable = config("exe", namespace = "xhmm", default = "xhmm")
def versionCommand = executable + "--version"
def versionCommand = executable + required("--version")
def versionRegex = """xhmm (.*)""".r
}
......@@ -78,6 +78,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
xhmmMethod.foreach { method =>
method.inputBams = inputBams
method.outputDir = new File(outputDir, "xhmm_method")
add(method)
}
addSummaryJobs()
......
......@@ -95,6 +95,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
genotype.inputXcnv = discover.outputXcnv
genotype.inputMatrix = secondMatrix.outputMatrix
genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
add(genotype)
addSummaryJobs()
......
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