Commit 68c080d8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed input and output

parent 08e62c12
......@@ -17,21 +17,28 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/** Wrapper for the bgzip command */
class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input files", required = !inputAsStdin)
@Input(doc = "Input files", required = false)
var input: List[File] = Nil
@Output(doc = "Compressed output file", required = !outputAsStsout)
@Output(doc = "Compressed output file", required = false)
var output: File = null
var f: Boolean = config("f", default = false)
executable = config("exe", default = "bgzip", freeVar = false)
override def beforeGraph(): Unit = {
super.beforeGraph()
if (input.isEmpty && ! inputAsStdin) Logging.addError("Input is missing in Bgzip")
if (output == null && ! outputAsStsout) Logging.addError("Output is missing in Bgzip")
}
def cmdLine = required(executable) +
conditional(f, "-f") +
" -c " + repeat(input) +
......
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