Commit 1c334578 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix compile errors

parent 412df3fe
......@@ -98,7 +98,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a stackbar plot for alignment stats
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -162,7 +162,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for insertsize
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -251,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for wgs coverage
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -342,7 +342,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for rna coverage
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......
......@@ -24,7 +24,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -44,7 +44,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
"variantcallers" -> variantcallers
)
lazy val shiva: ShivaTrait = new Shiva(qscript)
lazy val shiva = new Shiva(qscript)
def summaryFile: File = new File(outputDir, "Basty.summary.json")
......
......@@ -205,11 +205,12 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
logger.info(s"Starting script for ${samples.size} samples")
var count = 0
if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
samples.foreach { case (sampleId, sample) =>
logger.info(s"Starting script sample '$sampleId'")
sample.addAndTrackJobs()
count += 1
logger.info(s"Finish script for '$sampleId', samples done: $count / ${samples.size}")
samples.foreach {
case (sampleId, sample) =>
logger.info(s"Starting script sample '$sampleId'")
sample.addAndTrackJobs()
count += 1
logger.info(s"Finish script for '$sampleId', samples done: $count / ${samples.size}")
}
logger.info("Starting script for multisample jobs")
addMultiSampleJobs()
......
......@@ -189,7 +189,7 @@ trait ReportBuilder extends ToolCommand {
/**
* This method will render the page and the subpages recursivly
*
*
* @param summary The summary object
* @param page Page to render
* @param outputDir Root output dir of the report
......
......@@ -120,7 +120,7 @@ object ShivaReport extends MultisampleMappingReportTrait {
/**
* Generate a stackbar plot for found variants
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......
......@@ -22,7 +22,6 @@ import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordanc
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{ VarscanCnsSingleSample, _ }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
......
......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.gatk.broad._
......@@ -26,13 +26,13 @@ import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{ DataProvider, Test }
/**
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
class ShivaTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Shiva = {
new Shiva() {
......
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* 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
*/
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* 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.pipelines.shiva
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetPipe
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.broad.{HaplotypeCaller, UnifiedGenotyper}
import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer
/**
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
class ShivaVariantcallingTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
new ShivaVariantcalling() {
......@@ -55,7 +55,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
unifiedGenotyper <- bool;
haplotypeCaller <- bool
) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
).toArray
).toArray
}
@Test(dataProvider = "shivaVariantcallingOptions")
......
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