From 59459ae6757910c432d98873ba7db87b15003c6d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:40:18 +0200
Subject: [PATCH] Added Ln wrapper
---
.../nl/lumc/sasc/biopet/wrappers/Ln.scala | 25 +++++++++++++++++++
1 file changed, 25 insertions(+)
create mode 100644 biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala
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 000000000..f09971730
--- /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
--
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