diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala new file mode 100644 index 0000000000000000000000000000000000000000..f0997173015f16b05bf73daddbb6fbcb10feb244 --- /dev/null +++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala @@ -0,0 +1,25 @@ +package nl.lumc.sasc.biopet.wrappers + +import nl.lumc.sasc.biopet.core._ +import org.broadinstitute.sting.queue.function.CommandLineFunction +//import org.broadinstitute.sting.queue.function.QFunction +import org.broadinstitute.sting.commandline._ +import java.io.File + +class Ln(val globalConfig: Config) extends CommandLineFunction { + def this() = this(new Config(Map())) + this.analysisName = "ln" + val config: Config = globalConfig.getAsConfig(this.analysisName) + logger.debug("Config for " + this.analysisName + ": " + config) + + @Input(doc="Input file") var in: File = _ + @Output(doc="Link destination") var out: File = _ + + def commandLine = "ln -sf %s %s".format(in, out) +} + +object Ln { + def addLn(input:File, output:File) : Ln = { + return new Ln { this.in = input; this.out = output } + } +} \ No newline at end of file