From f9d9430b4d0e448c686a5ad7b971d875baa1ec42 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:41:20 +0200
Subject: [PATCH] Added Summarize flexiprep wrapper
---
.../flexiprep/scripts/Summarize.scala | 42 +++++++++++++++++++
1 file changed, 42 insertions(+)
create mode 100644 flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
new file mode 100644
index 000000000..fec2feccc
--- /dev/null
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
@@ -0,0 +1,42 @@
+package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
+
+import nl.lumc.sasc.biopet.core._
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import nl.lumc.sasc.biopet.wrappers.Python
+import org.broadinstitute.sting.commandline._
+import java.io.File
+
+class Summarize(val globalConfig: Config) extends CommandLineFunction with Python {
+ def this() = this(new Config(Map()))
+ analysisName = "flexiprep_sumarize"
+ val config: Config = globalConfig.getAsConfig(analysisName)
+ logger.debug("Config for " + analysisName + ": " + config)
+
+ setPythonScript("__init__.py", "scripts/pyfastqc/")
+ setPythonScript("summarize_flexiprep.py", "scripts/")
+
+ @Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
+ @Output(doc="Output file", shortName="out", required=true) var out: File = _
+
+ var samplea: String = _
+ var sampleb: String = _
+ var runDir: String = _
+ var samplename: String = _
+ var trim: Boolean = true
+ var clip: Boolean = true
+
+ def commandLine = {
+ var mode: String = ""
+ if (clip) mode += "clip"
+ if (trim) mode += "trim"
+ if (mode.isEmpty) mode = "none"
+
+ getPythonCommand +
+ optional("--run-dir", runDir) +
+ optional("--sampleb", sampleb) +
+ required(samplename) +
+ required(mode) +
+ required(samplea) +
+ required(out)
+ }
+}
\ No newline at end of file
--
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