BedtoolsSort.scala 681 Bytes
Newer Older
Sander Bollen's avatar
Sander Bollen committed
1 2 3 4 5 6
package nl.lumc.sasc.biopet.extensions.bedtools

import java.io.File

import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
Sander Bollen's avatar
Sander Bollen committed
7
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
Sander Bollen's avatar
Sander Bollen committed
8 9

/**
Sander Bollen's avatar
Sander Bollen committed
10 11
 * Created by Sander Bollen on 26-5-16.
 */
Sander Bollen's avatar
Sander Bollen committed
12 13 14 15 16 17 18 19 20 21 22 23 24
class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {

  @Input
  var input: File = null

  @Output
  var output: File = null

  @Argument(required = false)
  var faidx: File = referenceFai

  def cmdLine = required(executable) + required("sort") + required("-i", input) +
    optional("-faidx", faidx) +
Sander Bollen's avatar
Sander Bollen committed
25
    (if (outputAsStsout) "" else " > " + required(output))
Sander Bollen's avatar
Sander Bollen committed
26 27

}