From 157d6e8dedf5ab5617a79552dd10b20dc00b4a34 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:40:34 +0200
Subject: [PATCH] Added Sha1sum wrapper
---
.../nl/lumc/sasc/biopet/wrappers/Sha1sum.scala | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
create mode 100644 biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
new file mode 100644
index 000000000..d89e3d9ef
--- /dev/null
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala
@@ -0,0 +1,18 @@
+package nl.lumc.sasc.biopet.wrappers
+
+import nl.lumc.sasc.biopet.core._
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.commandline._
+import java.io.File
+
+class Sha1sum(val globalConfig: Config) extends CommandLineFunction {
+ def this() = this(new Config(Map()))
+ this.analysisName = "sha1sum"
+ val config: Config = globalConfig.getAsConfig("sha1sum")
+ logger.debug("Config for " + this.analysisName + ": " + config)
+
+ @Input(doc="Zipped file") var in: File = _
+ @Output(doc="Unzipped file") var out: File = _
+
+ def commandLine = "sha1sum %s > %s".format(in, out)
+}
\ No newline at end of file
--
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