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Commit 7cad5b3f authored by Peter van 't Hof's avatar Peter van 't Hof
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Added empty pipeline for bam metrics

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bam-metrics/.gitignore 0 → 100644
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/target/
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bam-metrics/examples/test.json 0 → 100644
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{
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"gatk": {"flexiprep": { "sdfg": { "exe": "gatk" }}},
"pbzip2": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"flexiprep": {
"fastqc": { "exe": "/home/pjvan_thof/pipelines/test/test" },
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
}
}
bam-metrics/pom.xml 0 → 100644
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<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Bam-Metrics</artifactId>
<version>0.1.3</version>
<packaging>jar</packaging>
<name>Bam-Metrics</name>
<url>http://maven.apache.org</url>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.1.3</version>
<relativePath>../</relativePath>
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<sting.unpack.phase>prepare-package</sting.unpack.phase>
<sting.shade.phase>package</sting.shade.phase>
<app.main.class>nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics</app.main.class>
</properties>
<dependencies>
<!-- <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>-->
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-compiler</artifactId>
<version>2.11.0</version>
</dependency>
<!-- <dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.9.2</artifactId>
<version>2.0.M4</version>
<scope>test</scope>
</dependency>-->
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId>
<version>0.1.3</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>queue-package</artifactId>
<version>3.1</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>scripts</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
<version>2.15.2</version>
<executions>
<execution>
<id>scala-compile</id>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
<configuration>
<args>
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
</args>
</configuration>
</execution>
</executions>
</plugin>
<!-- <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7.2</version>
<executions>
<execution>
<id>default-test</id>
Disable the default-test by putting it in phase none
<phase>none</phase>
</execution>
</executions>
</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>${project.artifactId}-${project.version}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${app.main.class}</Main-Class>
<X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
<X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
</manifestEntries>
</transformer>
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.sting:queue-package</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
<exclude>org.scala-lang:scala-reflect</exclude>
<exclude>org.scala-lang.modules:*</exclude>
</excludes>
</artifactSet>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 0 → 100644
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package nl.lumc.sasc.biopet.pipelines.bammetrics
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.picard._
import org.broadinstitute.sting.queue.function._
import org.broadinstitute.sting.commandline._
class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
def this() = this(null)
@Input(doc="Bam File", shortName="BAM",required=true)
var input_bam: File = _
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
}
def biopetScript() {
}
}
object BamMetrics extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.class"
}
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