diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala index 96ab2c89c629c0f2895c1e580eda1a477dcc96e2..84876820d0d025a2134a3e76ffcf70aa2988092c 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala @@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output } class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference { executable = config("exe", submodule = "perl", default = "perl") - var vep_script: String = config("vep_script") + var vepScript: String = config("vep_script") @Input(doc = "input VCF", required = true) var input: File = null @@ -37,7 +37,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu var output: File = null override def versionRegex = """version (\d*)""".r - override def versionCommand = executable + " " + vep_script + " --help" + override def versionCommand = executable + " " + vepScript + " --help" //Boolean vars var v: Boolean = config("v", default = true) @@ -152,7 +152,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu /** Returns command to execute */ def cmdLine = required(executable) + - required(vep_script) + + required(vepScript) + required("-i", input) + required("-o", output) + conditional(v, "-v") +