Commit 8e0d255e authored by Peter van 't Hof's avatar Peter van 't Hof

Init of tinycap

parent 28a34d76
<?xml version="1.0" encoding="UTF-8"?>
<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">
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.6.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>TinyCap</artifactId>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
package nl.lumc.sasc.biopet.pipelines.tinycap
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/29/15.
*/
class TinyCap(val root: Configurable) extends QScript with MultisampleMappingTrait with Reference {
qscript =>
def this() = this(null)
override def defaults = Map(
"mapping" -> Map("alinger" -> "bowtie"),
"bowtie" -> Map(
"chunkmbs" -> 256,
"seedmms" -> 3,
"seedlen" -> 25,
"k" -> 5,
"best" -> true)
)
override def summaryFile = new File(outputDir, "tinycap.summary.json")
}
object TinyCap extends PipelineCommand
\ No newline at end of file
......@@ -64,6 +64,11 @@
<artifactId>Gentrap</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>TinyCap</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Sage</artifactId>
......
......@@ -24,6 +24,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping,
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
nl.lumc.sasc.biopet.pipelines.tinycap.TinyCap,
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
nl.lumc.sasc.biopet.pipelines.sage.Sage,
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig,
......
......@@ -46,6 +46,7 @@
<module>biopet-tools-extensions</module>
<module>biopet-extensions</module>
<module>biopet-tools-package</module>
<module>TinyCap</module>
</modules>
<properties>
......
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