From 50dc06bb9d66b2dd81886f7a72ab85a6736de7f5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Jun 2014 09:40:27 +0200
Subject: [PATCH] deps not required
---
.../sasc/biopet/wrappers/fastq/Sickle.scala | 19 ++-----------------
1 file changed, 2 insertions(+), 17 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
index 156c2cefa..b8a9d5335 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala
@@ -22,7 +22,7 @@ class Sickle(val globalConfig: Config) extends CommandLineFunction {
@Output(doc="stats output") var output_stats: File = null
@Input(doc="qualityType file", required=false) var qualityTypeFile: File = null
@Argument(doc="Quality Type", required=false) var qualityType: String = config.getAsString("qualitytype", null)
- @Input(doc="deps") var deps: List[File] = Nil
+ @Input(doc="deps", required=false) var deps: List[File] = Nil
var defaultQualityType: String = config.getAsString("defaultqualitytype", "sanger")
@@ -59,22 +59,7 @@ class Sickle(val globalConfig: Config) extends CommandLineFunction {
} else logger.warn("File : " + qualityTypeFile + " does not exist")
}
}
-
-// private var version: String = _
-// def getVersion : String = {
-// val REG = """sickle version (.*)""".r
-// if (version == null) for (line <- (sickle_exe + " --version").!!.split("\n")) {
-// line match {
-// case REG(m) => {
-// version = m
-// return version
-// }
-// case _ =>
-// }
-// }
-// return version
-// }
-
+
private var version: String = _
var versionCommand = sickle_exe + " --version"
var versionRegex = """sickle version (.*)"""
--
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