Commit 44703a46 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

No functional changes

parent 32c7c09f
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.1.0</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId>
......@@ -28,16 +33,6 @@
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7.2</version>
<executions>
<execution>
<id>default-test</id>
<phase>none</phase>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
......
......@@ -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
......@@ -73,6 +73,20 @@
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.9.2</artifactId>
<version>2.0.M4</version>
<scope>test</scope>
</dependency>
</dependencies>
<properties>
<app.main.class>nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep</app.main.class>
<sting.shade.phase>package</sting.shade.phase>
......
......@@ -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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