From 08a62d84e076fd890bbfba1d907eb66bf830786f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Jun 2014 11:51:12 +0200
Subject: [PATCH] No functional changes
---
.../nl/lumc/sasc/biopet/wrappers/Zcat.scala | 18 +++++++++---------
flexiprep/examples/test.json | 1 +
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
index 8c0e3de2d..de8b4efdc 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala
@@ -6,13 +6,13 @@ import org.broadinstitute.sting.commandline._
import java.io.File
class Zcat(val globalConfig: Config) extends CommandLineFunction {
- def this() = this(new Config(Map()))
- this.analysisName = "zcat"
- val config: Config = globalConfig.getAsConfig("zcat")
- logger.debug("Config for " + this.analysisName + ": " + config)
-
- @Input(doc="Zipped file") var in: File = _
- @Output(doc="Unzipped file") var out: File = _
-
- def commandLine = "zcat %s > %s".format(in, out)
+ def this() = this(new Config(Map()))
+ this.analysisName = "zcat"
+ val config: Config = globalConfig.getAsConfig("zcat")
+ logger.debug("Config for " + this.analysisName + ": " + config)
+
+ @Input(doc="Zipped file") var in: File = _
+ @Output(doc="Unzipped file") var out: File = _
+
+ def commandLine = "zcat %s > %s".format(in, out)
}
\ No newline at end of file
diff --git a/flexiprep/examples/test.json b/flexiprep/examples/test.json
index 59469ffd4..9a50037ee 100644
--- a/flexiprep/examples/test.json
+++ b/flexiprep/examples/test.json
@@ -2,6 +2,7 @@
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"flexiprep": {
+ "native_link": true,
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
--
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