From 7cad5b3fb512ce4ba3fcbac76abb39149c300b64 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 27 Jun 2014 13:38:10 +0200
Subject: [PATCH] Added empty pipeline for bam metrics
---
bam-metrics/.gitignore | 1 +
bam-metrics/examples/test.json | 10 ++
bam-metrics/pom.xml | 135 ++++++++++++++++++
.../pipelines/bammetrics/BamMetrics.scala | 27 ++++
4 files changed, 173 insertions(+)
create mode 100644 bam-metrics/.gitignore
create mode 100644 bam-metrics/examples/test.json
create mode 100644 bam-metrics/pom.xml
create mode 100644 bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
diff --git a/bam-metrics/.gitignore b/bam-metrics/.gitignore
new file mode 100644
index 000000000..a6f89c2da
--- /dev/null
+++ b/bam-metrics/.gitignore
@@ -0,0 +1 @@
+/target/
\ No newline at end of file
diff --git a/bam-metrics/examples/test.json b/bam-metrics/examples/test.json
new file mode 100644
index 000000000..285265ef0
--- /dev/null
+++ b/bam-metrics/examples/test.json
@@ -0,0 +1,10 @@
+{
+ "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"}
+ }
+}
diff --git a/bam-metrics/pom.xml b/bam-metrics/pom.xml
new file mode 100644
index 000000000..bad58c52d
--- /dev/null
+++ b/bam-metrics/pom.xml
@@ -0,0 +1,135 @@
+<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>
diff --git a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
new file mode 100644
index 000000000..f80e958b9
--- /dev/null
+++ b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -0,0 +1,27 @@
+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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