Commit de951794 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added version tag for vep

parent e0e53ed2
......@@ -14,7 +14,7 @@
*/
package nl.lumc.sasc.biopet.core.annotations
import nl.lumc.sasc.biopet.core.{BiopetQScript, Reference}
import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference }
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.utils.LazyCheck
import org.broadinstitute.gatk.queue.QScript
......
......@@ -39,6 +39,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
@Output(doc = "output file", required = true)
var output: File = null
override def subPath = super.subPath ++ vepConfig
def versionRegex = """version (\d*)""".r
def versionCommand = executable + " " + vepScript + " --help"
......@@ -106,7 +108,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var skibDbCheck: Boolean = config("skip_db_check", default = false)
// Textual args
var vepConfig: Option[String] = config("config", freeVar = false)
var vepConfigArg: 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")
......@@ -229,7 +231,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
conditional(lrg, "--lrg") +
conditional(noWholeGenome, "--no_whole_genome") +
conditional(skibDbCheck, "--skip_db_check") +
optional("--config", vepConfig) +
optional("--config", vepConfigArg) +
optional("--species", species) +
optional("--assembly", assembly) +
optional("--format", format) +
......
......@@ -149,7 +149,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with Scat
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
knownSites ::= dbsnpVcfFile
dbsnpVcfFile.foreach(knownSites :+= _)
override def beforeGraph() {
super.beforeGraph()
......
......@@ -68,7 +68,7 @@ class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK wit
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = config("", default = false)
known ::= dbsnpVcfFile
dbsnpVcfFile.foreach(known :+= _)
override def beforeGraph() {
super.beforeGraph()
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment