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

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>
......
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