Commit f3343df9 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix pipeline without framework

parent 3bf08752
......@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......
......@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
......
......@@ -11,7 +11,7 @@ import com.google.common.io.Files
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.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -30,7 +30,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -5,7 +5,8 @@
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.core.{BiopetExecutable, MainCommand}
import nl.lumc.sasc.biopet.core.BiopetExecutable
import nl.lumc.sasc.biopet.utils.MainCommand
object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
......
......@@ -37,7 +37,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import nl.lumc.sasc.biopet.scripts.CoverageStats
import nl.lumc.sasc.biopet.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import org.broadinstitute.gatk.queue.QScript
class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......
......@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import nl.lumc.sasc.biopet.scripts.CoverageStats
import nl.lumc.sasc.biopet.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -42,7 +42,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -25,7 +25,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
trait BastyTrait extends MultiSampleQScript {
......
......@@ -41,6 +41,12 @@
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
<version>3.4</version>
<exclusions>
<exclusion>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gsalib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
......
......@@ -41,7 +41,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -15,7 +15,8 @@
*/
package nl.lumc.sasc.biopet
import nl.lumc.sasc.biopet.core.{BiopetExecutable, MainCommand}
import nl.lumc.sasc.biopet.core.BiopetExecutable
import nl.lumc.sasc.biopet.utils.MainCommand
object BiopetExecutablePublic extends BiopetExecutable {
def publicPipelines: List[MainCommand] = List(
......
......@@ -47,7 +47,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
}
}
object Seqstat {
object SeqStat {
def apply(root: Configurable, input: File, output: File): SeqStat = {
val seqstat = new SeqStat(root)
seqstat.input = input
......
......@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -15,11 +15,11 @@
*/
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......
......@@ -19,8 +19,8 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
val builder = FlexiprepReport
......
......@@ -20,7 +20,7 @@ import java.io.File
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.{ Gzip, Sickle, Zcat }
import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -32,7 +32,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -16,7 +16,6 @@
package nl.lumc.sasc.biopet.pipelines.gears
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
......@@ -25,7 +24,7 @@ import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDupli
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.extensions.tools.FastqSync
import org.broadinstitute.gatk.queue.QScript
import scala.collection.JavaConversions._
......
......@@ -33,11 +33,6 @@
<name>Gentrap</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
......
......@@ -29,7 +29,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function.QFunction
......
......@@ -18,10 +18,11 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.varscan.Mpileup2cns
import nl.lumc.sasc.biopet.extensions.{ Bgzip, PythonCommandLineFunction, Tabix }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.language.reflectiveCalls
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.{ File, FileOutputStream }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
......@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import nl.lumc.sasc.biopet.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping.scripts
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.pipelines.flexiprep.{ Cutadapt, Fastqc, SeqtkSeq }
import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -25,7 +25,7 @@
<version>0.5.0-SNAPSHOT</version>
<modules>
<module>biopet-framework</module>
<!--<module>biopet-framework</module>-->
<module>biopet-public-package</module>
<module>bammetrics</module>
<module>flexiprep</module>
......
......@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -22,8 +22,8 @@ import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.tools.SquishBed
import nl.lumc.sasc.biopet.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
import nl.lumc.sasc.biopet.extensions.tools.SquishBed
import nl.lumc.sasc.biopet.extensions.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......
......@@ -32,7 +32,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
......
......@@ -15,18 +15,16 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.tools.VcfStats
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.Input
import scala.collection.JavaConversions._
/**
......@@ -70,7 +68,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
def biopetScript(): Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
}
val callers = callersList.filter(x => configCallers.contains(x.name))
......
......@@ -18,13 +18,13 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
......@@ -62,7 +62,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
def biopetScript(): Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
}
val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
......
......@@ -21,7 +21,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
......
......@@ -21,7 +21,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
......
......@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.extensions.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......
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