diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala index 287639df1197b46c122aebc55b6760a534cb1057..0c744344f104c7f95afa4f0de92693f82620bbd9 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala @@ -18,31 +18,31 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK { @Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written") var out: File = _ + @Output private var _summaryFile: File = _ + @Output private var _statisticsFile: File = _ + @Output private var _intervalSummaryFile: File = _ + @Output private var _intervalStatisticsFile: File = _ + @Output private var _geneSummaryFile: File = _ + @Output private var _geneStatisticsFile: File = _ + @Output private var _cumulativeCoverageCountsFile: File = _ + @Output private var _cumulativeCoverageProportionsFile: File = _ - @Output - var summaryFile = _summaryFile - @Output - var statisticsFile = _statisticsFile - @Output - var intervalSummaryFile = _intervalSummaryFile - @Output - var intervalStatisticsFile = _intervalStatisticsFile - @Output - var geneSummaryFile = _geneSummaryFile - @Output - var geneStatisticsFile = _geneStatisticsFile - @Output - var culumativeCoverageCountsFile = _cumulativeCoverageCountsFile - @Output - var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile + def summaryFile = new File(out + ".sample_summary") + def statisticsFile = new File(out + ".sample_statistics") + def intervalSummaryFile = new File(out + ".sample_interval_summary") + def intervalStatisticsFile = new File(out + ".sample_interval_statistics") + def geneSummaryFile = new File(out + ".sample_gene_summary") + def geneStatisticsFile = new File(out + ".sample_gene_statistics") + def cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts") + def cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions") @Input(required = false) var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None) @@ -92,14 +92,14 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK { if (out == null) { throw new IllegalStateException("You must set the variable") } - _summaryFile = new File(out + ".sample_summary") - _statisticsFile = new File(out + ".sample_statistics") - _intervalSummaryFile = new File(out + ".sample_interval_summary") - _intervalStatisticsFile = new File(out + ".sample_interval_statistics") - _geneSummaryFile = new File(out + ".sample_gene_summary") - _geneStatisticsFile = new File(out + ".sample_gene_statistics") - _cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts") - _cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions") + _summaryFile = summaryFile + _statisticsFile = statisticsFile + _intervalSummaryFile = intervalSummaryFile + _intervalStatisticsFile = intervalStatisticsFile + _geneSummaryFile = geneSummaryFile + _geneStatisticsFile = geneStatisticsFile + _cumulativeCoverageCountsFile = cumulativeCoverageCountsFile + _cumulativeCoverageProportionsFile = cumulativeCoverageProportionsFile } override def cmdLine = { diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala index f61e0d179c4525c582d884521058af55ddb756e9..f0502b713bea21f8c4e9ea933bfc5aecb141f7b0 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala @@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable { @Input var r: File = _ + @Output private var _outputXcnvAuxFile: File = _ - @Output - var outputXcnvAuxFile = _outputXcnvAuxFile + def outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux") var xhmmAnalysisName: String = _ @@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable { if (outputXcnv == null) { throw new IllegalStateException("Must set output file") } - _outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux") + _outputXcnvAuxFile = outputXcnvAuxFile } def cmdLine = { diff --git a/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala b/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala index 19cc27b4fcc253e7b50740e9c72747ad22f2ac69..bf2239b6b1924c06666117de0ea0f3d8ddc29526 100644 --- a/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala +++ b/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala @@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { def biopetScript() = { val depths = inputBams.map { keyValuePair => - DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, ".bam", ".dcov"), List(targets)) + DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, keyValuePair._2, ".bam", ".dcov"), List(targets)) }.toList addAll(depths)