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Commit 0acd0e4b authored by Peter van 't Hof's avatar Peter van 't Hof
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Added gentrap as artifact

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public/gentrap/.gitignore 0 → 100644
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/target/
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public/gentrap/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>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 0 → 100644
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/**
* 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
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