Commit 69a3c90f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Name fix

parent 2fe05703
......@@ -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") +
......
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