Commit 1a106737 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-star_version' into 'develop'

Added version command for star

Only need to be tested

See merge request !271
parents 3925dac1 bcadec7e
......@@ -18,13 +18,13 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Extension for STAR
*/
class Star(val root: Configurable) extends BiopetCommandLineFunction with Reference {
class Star(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "The reference file for the bam files.", required = false)
var reference: File = null
......@@ -54,6 +54,9 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
executable = config("exe", "STAR")
def versionCommand = executable + " --version"
def versionRegex = """(.*)""".r
@Argument(doc = "Output Directory")
var outputDir: File = _
......
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