diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala index ab43444f17ef2710c91c6a0097021386cc7e0357..5b277059e09ca6ad269bf5e7adebcef3a8176fee 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala @@ -38,17 +38,16 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit @Input(doc = "Reference") var reference: File = _ - protected def cleverOutputDir: File = new File(cleverWorkDir, "work") var cleverWorkDir: File = _ @Output(doc = "Clever VCF output") lazy val outputvcf: File = { - new File(cleverOutputDir, "predictions.vcf") + new File(cleverWorkDir, "predictions.vcf") } @Output(doc = "Clever raw output") lazy val outputraw: File = { - new File(cleverOutputDir, "predictions.raw.txt") + new File(cleverWorkDir, "predictions.raw.txt") } // var T: Option[Int] = config("T", default = defaultThreads) @@ -60,13 +59,13 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit override def beforeGraph() { super.beforeGraph() - if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined") + if (cleverWorkDir == null) throw new Exception("Clever :: Workdirectory is not defined") if (reference == null) reference = referenceFasta() } def cmdLine = required(executable) + - " --sorted " + - " --use_xa " + + required("--sorted") + + required("--use_xa") + optional("-T", threads) + conditional(f, "-f") + conditional(a, "-a") + @@ -74,7 +73,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit conditional(r, "-r") + required(input) + required(reference) + - required(cleverOutputDir) + required(cleverWorkDir) } object CleverCaller { diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala index ba0b0fc9a2c6f8f80abeb44fe5d7254089cefd8e..adc99e9fa9d7daadd9405f06df745edd4f7f264f 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala +++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala @@ -23,10 +23,10 @@ class Clever(val root: Configurable) extends SvCaller { def name = "clever" def biopetScript() { - //TODO: check double directories for ((sample, bamFile) <- inputBams) { val cleverDir = new File(outputDir, sample) - val clever = CleverCaller(this, bamFile, cleverDir) + val clever = CleverCaller(this, bamFile, new File(cleverDir, "clever_output")) + clever.jobOutputFile = new File(cleverDir, ".CleverCaller.out") add(clever) val cleverVCF = new CleverFixVCF(this)