Commit a6e1f2bc authored by Sander Bollen's avatar Sander Bollen
Browse files

afterGraph was deprecated, now beforeGraph

parent 3a8de40e
......@@ -12,13 +12,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", submodule = "perl", default = "perl")
var vep_script: String = config("vep_script", required = true)
var vep_script: String = config("vep_script")
@Input(doc = "input VCF", required = true)
var input: File = _
var input: File = null
@Output(doc = "output file", required = true)
var output: File = _
var output: File = null
override val versionRegex = """version (\d*)""".r
override def versionCommand = executable + " " + vep_script + " --help"
......@@ -125,8 +125,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var db_version: Option[Int] = config("db_version")
var buffer_size: Option[Int] = config("buffer_size")
override def afterGraph: Unit = {
super.afterGraph
override def beforeGraph: Unit = {
super.beforeGraph
if (!cache && !database) {
throw new IllegalArgumentException("Must supply either cache or database")
} else if (cache && dir.isEmpty) {
......
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