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