Commit 02639191 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent 05233c6b
......@@ -5,8 +5,8 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvan_thof on 11/20/15.
*/
* Created by pjvan_thof on 11/20/15.
*/
trait TargetRegions extends Configurable {
/** Bed files for region of interests */
var roiBedFiles: List[File] = config("regions_of_interest", Nil)
......
......@@ -135,7 +135,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
that.biopetScript()
this match {
case s: SummaryQScript => s.addSummaryQScript(that)
case _ =>
case _ =>
}
case that: BiopetQScript =>
that.init()
......
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.vt
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract class Vt extends BiopetCommandLineFunction {
override def subPath = "vt" :: super.subPath
executable = config("exe", default = "vt")
......
......@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, Version}
import nl.lumc.sasc.biopet.core.{ Reference, Version }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 20/11/15.
*/
* Created by pjvanthof on 20/11/15.
*/
class VtDecompose(val root: Configurable) extends Vt with Version with Reference {
def versionRegex = """decompose (.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, Version}
import nl.lumc.sasc.biopet.core.{ Reference, Version }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvanthof on 20/11/15.
*/
* Created by pjvanthof on 20/11/15.
*/
class VtNormalize(val root: Configurable) extends Vt with Version with Reference {
def versionRegex = """normalize (.*)""".r
override def versionExitcode = List(0, 1)
......
......@@ -116,7 +116,8 @@ object ShivaReport extends MultisampleReportBuilder {
)).toList.sortBy(_._1),
List(),
Map())
) else None
)
else None
}
/** Files page, can be used general or at sample level */
......@@ -192,7 +193,7 @@ object ShivaReport extends MultisampleReportBuilder {
def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
val path = target match {
case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
}
val homVar = new SummaryValue(path :+ "HomVar", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val homRef = new SummaryValue(path :+ "HomRef", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
......
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{Delly, Breakdancer, Clever, SvCaller}
import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......
......@@ -19,7 +19,7 @@ import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, Reference }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, SamToFastq }
import nl.lumc.sasc.biopet.pipelines.bammetrics.{TargetRegions, BamMetrics}
import nl.lumc.sasc.biopet.pipelines.bammetrics.{ TargetRegions, BamMetrics }
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import nl.lumc.sasc.biopet.utils.Logging
......
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
......
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerVCF, BreakdancerCaller, BreakdancerConfig}
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerCaller, BreakdancerConfig }
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Breakdancer */
......
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript }
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 23/11/15.
*/
* Created by pjvanthof on 23/11/15.
*/
trait SvCaller extends QScript with BiopetQScript with Reference {
/** Name of mode, this should also be used in the config */
......
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