Commit c0a2280c authored by Peter van 't Hof's avatar Peter van 't Hof

Switched Basty to Shiva

parent aab08ec8
......@@ -39,6 +39,11 @@
<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>
......
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
......@@ -11,7 +11,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.Shiva,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.basty.Basty)
nl.lumc.sasc.biopet.pipelines.gatk.Basty)
def tools = BiopetExecutablePublic.tools
}
\ No newline at end of file
......@@ -20,7 +20,6 @@
<modules>
<module>biopet-gatk-extensions</module>
<module>biopet-gatk-pipelines</module>
<module>basty</module>
<module>biopet-protected-package</module>
</modules>
</project>
\ No newline at end of file
......@@ -31,7 +31,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkPipelines</artifactId>
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
package nl.lumc.sasc.biopet.pipelines.basty
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 3/4/15.
*/
class Basty(val root: Configurable) extends QScript with BastyTrait {
def this() = this(null)
}
object Basty extends PipelineCommand
\ No newline at end of file
......@@ -8,17 +8,13 @@ package nl.lumc.sasc.biopet.pipelines.basty
import java.io.File
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.{ RunGubbins, Cat, Raxml }
import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, Shiva }
import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
trait BastyTrait extends MultiSampleQScript {
qscript =>
def this() = this(null)
case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
......@@ -26,10 +22,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
override def defaults = ConfigUtils.mergeMaps(Map(
"ploidy" -> 1,
"variantscallers" -> variantcallers
"variantcallers" -> variantcallers
), super.defaults)
val shiva = new Shiva(qscript)
lazy val shiva: ShivaTrait = new Shiva(qscript)
def summaryFile: File = new File(outputDir, "Sage.summary.json")
......@@ -114,7 +110,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val raxmlMl = new Raxml(this)
raxmlMl.input = variants
raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlMl.p = seed
raxmlMl.p = Some(seed)
raxmlMl.n = outputName + "_ml"
raxmlMl.w = dirSufixRaxml
raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
......@@ -127,10 +123,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBoot.threads = 1
raxmlBoot.input = variants
raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBoot.p = seed
raxmlBoot.b = math.abs(r.nextInt)
raxmlBoot.p = Some(seed)
raxmlBoot.b = Some(math.abs(r.nextInt))
raxmlBoot.w = dirSufixRaxml
raxmlBoot.N = 1
raxmlBoot.N = Some(1)
raxmlBoot.n = outputName + "_boot_" + t
add(raxmlBoot)
raxmlBoot.getBootstrapFile
......@@ -144,7 +140,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBi.t = raxmlMl.getBestTreeFile
raxmlBi.z = cat.output
raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBi.p = seed
raxmlBi.p = Some(seed)
raxmlBi.f = "b"
raxmlBi.n = outputName + "_bi"
raxmlBi.w = dirSufixRaxml
......@@ -181,5 +177,3 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
return FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
}
}
object Basty extends PipelineCommand
......@@ -100,6 +100,11 @@
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
......
......@@ -31,7 +31,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
def pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.basty.Basty
) ::: protectedPipelines
def tools: List[MainCommand] = List(
......
......@@ -38,6 +38,7 @@
<module>carp</module>
<module>toucan</module>
<module>shiva</module>
<module>basty</module>
</modules>
<properties>
......
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