Added gentrap as artifact

public/gentrap/.gitignore

+/target/
\ No newline at end of file

public/gentrap/pom.xml

+<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>Gentrap</artifactId>
+    <version>0.2.0-DEV</version>
+    <packaging>jar</packaging>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>Gentrap</name>
+    <url>http://maven.apache.org</url>
+
+    <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.core.BiopetExecutable</app.main.class>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Mapping</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</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>
+                                <arg>-deprecation</arg>
+                                <arg>-feature</arg>
+                            </args>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>2.5</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <showDeprecation>true</showDeprecation>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author Wibowo Arindrarto
+ */
+
+package nl.lumc.sasc.biopet.pipelines.gentrap
+
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk._
+import org.broadinstitute.gatk.queue.extensions.picard._
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+
+/**
+ * Gentrap pipeline
+ * Generic transcriptome analysis pipeline
+ */
+class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
+
+  def this() = this(null)
+
+  /** Read 1 input */
+  @Input(doc = "FASTQ file input (single-end or pair 1)", fullName = "input_r1", shortName = "R1", required = true)
+  var inputR1: File = _
+
+  /** Read 2 input (optional) */
+  @Input(doc = "FASTQ file input (pair 2)", fullName = "input_r2", shortName = "R2", required = false)
+  var inputR2: File = _
+
+  /** Split aligner to use */
+  @Argument(doc = "Split aligner", fullName = "aligner", shortName = "aln", required = true, validation = "gsnap|tophat|star")
+  var aligner: String = _
+
+  /** Whether library is strand-specifc (dUTP protocol) or not */
+  @Argument(doc = "Whether input data was made using the dUTP strand-specific protocol", fullName = "strand_specific", shortName = "strandSpec", required = true)
+  var strandSpec: Boolean = _
+
+  /** Variant calling */
+  @Argument(doc = "Variant caller", fullName = "variant_caller", shortName = "varCaller", required = false, validation = "varscan|snvmix")
+  var varcaller: String = _
+
+  /** Cufflinks assembly type */
+  @Argument(doc = "Cufflinks assembly type", fullName = "transcript_asm", shortName = "transAsm", required = false, validation = "none|strict|guided|blind")
+  var asm: List[String] = List("none")
+
+  /** FASTQ trimming */
+  @Argument(doc = "Whether to skip trimming input files", fullName = "skip_trim_input", shortName = "skipTrim", required = false)
+  var skipTrim: Boolean = false
+
+  /** FASTQ clipping */
+  @Argument(doc = "Whether to skip clipping input files", fullName = "skip_clip_input", shortName = "skipClip", required = false)
+  var skipClip: Boolean = false
+
+  /** Gene-wise read count table output */
+  @Argument(doc = "Gene read count table output", fullName = "count_gene_read", shortName = "cGeneRead", required = false)
+  var cGeneRead: Boolean = _
+
+  /** Gene-wise base count table output */
+  @Argument(doc = "Gene base count table output", fullName = "count_gene_base", shortName = "cGeneBase", required = false)
+  var cGeneBase: Boolean = _
+
+  /** Exon-wise base count table output */
+  @Argument(doc = "Exon base count table output", fullName = "count_exon_base", shortName = "cExonBase", required = false)
+  var cExonBase: Boolean = _
+
+  def init() {
+
+  }
+
+  def biopetScript() {
+  }
+}
+
+object Gentrap extends PipelineCommand