Commit 36e763df authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Make new package for bwa

parent 695650c2
package nl.lumc.sasc.biopet.extensions.bwa
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* Created by pjvan_thof on 1/16/15.
*/
abstract class Bwa extends BiopetCommandLineFunction {
override def subPath = "bwa" :: super.subPath
executable = config("exe", default = "bwa")
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
override def versionCommand = executable
}
......@@ -13,14 +13,15 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.aligners
package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
class BwaMem(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = _
......@@ -62,15 +63,9 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var Y: Boolean = config("Y", default = false)
var I: String = config("I")
executable = config("exe", default = "bwa", freeVar = false)
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
override val defaultVmem = "6G"
override val defaultThreads = 8
override def versionCommand = executable
def cmdLine = {
required(executable) +
required("mem") +
......
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