From a98ad7f77f7683aa9e4e874b3827c761cc08c9b4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:41:01 +0200
Subject: [PATCH] Added Seqstat wrapper
---
.../pipelines/flexiprep/scripts/Seqstat.scala | 30 +++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
new file mode 100644
index 000000000..003b07535
--- /dev/null
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -0,0 +1,30 @@
+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 Seqstat(val globalConfig: Config) extends CommandLineFunction with Python {
+ def this() = this(new Config(Map()))
+ analysisName = "seqstat"
+ val config: Config = globalConfig.getAsConfig(analysisName)
+ logger.debug("Config for " + analysisName + ": " + config)
+
+ setPythonScript("__init__.py", "scripts/pyfastqc/")
+ setPythonScript("seq_stat.py", "scripts/")
+
+ @Input(doc="Fastq input", shortName="fastqc", required=true) var input_fastq: File = _
+ @Input(doc="Dep", shortName="dep", required=false) var deps: List[File] = Nil
+ @Output(doc="Output file", shortName="out", required=true) var out: File = _
+
+ var fmt: String = _
+
+ def commandLine = {
+ getPythonCommand +
+ optional("--fmt", fmt) +
+ required("-o", out) +
+ required(input_fastq)
+ }
+}
--
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