Commit 4aac76ff authored by bow's avatar bow
Browse files

Merge branch 'feature-shiva' into 'develop'

Feature shiva

This will become a new version of the variantcalling pipeline.

See also issue #116 and #119

See merge request !110
parents 5586ca77 dc856bfa
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
......@@ -21,5 +21,5 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
if (config.contains("pedigree")) pedigree = config("pedigree")
}
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -3,7 +3,7 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.extensions.gatk
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
......
......@@ -39,5 +39,27 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.11</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 3/4/15.
*/
class Basty(val root: Configurable) extends QScript with BastyTrait {
qscript =>
def this() = this(null)
override def variantcallers = List("unifiedgenotyper")
override lazy val shiva = new Shiva(qscript)
}
object Basty extends PipelineCommand
\ No newline at end of file
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeGVCFs, SelectVariants }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
......
......@@ -10,9 +10,9 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
......
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