Commit b5500137 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-toucan' into 'develop'

Fix toucan



See merge request !279
parents 09e0d7e1 80917351
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
......@@ -40,8 +41,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
def versionCommand = executable + " " + vepScript + " --help"
//Boolean vars
var v: Boolean = config("v", default = true)
var q: Boolean = config("q", default = false)
var v: Boolean = config("v", default = true, freeVar = false)
var q: Boolean = config("q", default = false, freeVar = false)
var offline: Boolean = config("offline", default = false)
var no_progress: Boolean = config("no_progress", default = false)
var everything: Boolean = config("everything", default = false)
......@@ -76,8 +77,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var old_map: Boolean = config("old_maf", default = false)
var pubmed: Boolean = config("pubmed", default = false)
var vcf: Boolean = config("vcf", default = true)
var json: Boolean = config("json", default = false)
var vcf: Boolean = config("vcf", default = true, freeVar = false)
var json: Boolean = config("json", default = false, freeVar = false)
var gvf: Boolean = config("gvf", default = false)
var check_ref: Boolean = config("check_ref", default = false)
var coding_only: Boolean = config("coding_only", default = false)
......@@ -103,8 +104,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var skip_db_check: Boolean = config("skip_db_check", default = false)
// Textual args
var vep_config: Option[String] = config("config")
var species: Option[String] = config("species")
var vep_config: Option[String] = config("config", freeVar = false)
var species: Option[String] = config("species", freeVar = false)
var assembly: Option[String] = config("assembly")
var format: Option[String] = config("format")
var dir: Option[String] = config("dir")
......@@ -146,9 +147,9 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override def beforeGraph(): Unit = {
super.beforeGraph()
if (!cache && !database) {
throw new IllegalArgumentException("Must supply either cache or database for VariantEffectPredictor")
Logging.addError("Must supply either cache or database for VariantEffectPredictor")
} else if (cache && dir.isEmpty) {
throw new IllegalArgumentException("Must supply dir to cache for VariantEffectPredictor")
Logging.addError("Must supply dir to cache for VariantEffectPredictor")
}
}
......
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