Merge branch 'release-0.7.0' into 'master'

Release 0.7.0



See merge request !449

.gitignore

@@ -10,7 +10,5 @@ git.properties
 .idea/*
 *.iml
 target/
-public/target/
-protected/target/
 site/
 *.sc
\ No newline at end of file

README.md

@@ -55,18 +55,18 @@ At the moment, we do not provide links to download the Biopet package. If you ar
 
 ## Contributing to Biopet
 
-Biopet is based on the Queue framework developed by the Broad Institute as part of their Genome Analysis Toolkit (GATK) framework. The current Biopet release is based on the GATK 3.4 release.
+Biopet is based on the Queue framework developed by the Broad Institute as part of their Genome Analysis Toolkit (GATK) framework. The current Biopet release is based on the GATK 3.5 release.
 
 We welcome any kind of contribution, be it merge requests on the code base, documentation updates, or any kinds of other fixes! The main language we use is Scala, though the repository also contains a small bit of Python and R. Our main code repository is located at [https://github.com/biopet/biopet](https://github.com/biopet/biopet/issues), along with our issue tracker.
 
 ## Local development setup
 
-To develop Biopet, Java 7, Maven 3.2.2, and GATK Queue 3.4 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
+To develop Biopet, Java 7, Maven 3.3.3, and GATK Queue 3.5 is required. Please consult the Java homepage and Maven homepage for the respective installation instruction. After you have both Java and Maven installed, you would then need to install GATK Queue. However, as the GATK Queue package is not yet available as an artifact in Maven Central, you will need to download, compile, and install GATK Queue first.
 
 ~~~
 $ git clone https://github.com/broadgsa/gatk-protected
-$ cd gatk-protected
-$ git checkout 3.4                              # the current release is based on GATK 3.4
+$ cd gatk
+$ git checkout 3.5                              # the current release is based on GATK 3.5
 $ mvn -U clean install
 ~~~
 

bam2wig/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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 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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>Bam2Wig</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.7.0</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>Bam2Wig</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetExtensions</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala → bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala → bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

public/bam2wig/src/test/resources/log4j.properties → bam2wig/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

+/**
+ * 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 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.pipelines.bamtobigwig
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by pjvanthof on 09/05/16.
+ */
+class BamToChromSizesTest extends TestNGSuite with Matchers {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testChromSizes: Unit = {
+    val bamFile = new File(resourcePath("/empty.bam"))
+    val bamToChromSizes = new BamToChromSizes(null)
+    bamToChromSizes.bamFile = bamFile
+    bamToChromSizes.chromSizesFile = File.createTempFile("chrom.", ".sizes")
+    bamToChromSizes.chromSizesFile.deleteOnExit()
+    bamToChromSizes.run()
+    Source.fromFile(bamToChromSizes.chromSizesFile).getLines().toList shouldBe List("chrQ\t10000", "chrR\t10000")
+  }
+}

public/bammetrics/pom.xml → bammetrics/pom.xml

@@ -9,8 +9,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 
@@ -25,7 +24,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.6.0</version>
+        <version>0.7.0</version>
         <relativePath>../</relativePath>
     </parent>
     

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp → bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

@@ -63,6 +63,7 @@
         #if (!sampleLevel) <th>Library</th> #end
         <th>Total</th>
         <th>Mapped</th>
+        <th>Secondary</th>
         <th>(%)</th>
         <th>Duplicates</th>
         <th>(%)</th>
@@ -85,12 +86,14 @@
                         val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
                         val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
                         val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+                        val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
                     }#
                     <td>${total}</td>
                     <td>${mapped}</td>
-                    <td>${mapped.toDouble / total * 100}%</td>
+                    <td>${secondary}</td>
+                    <td>${(mapped - secondary).toDouble / (total - secondary) * 100}%</td>
                     <td>${duplicates}</td>
-                    <td>${duplicates.toDouble / total * 100}%</td>
+                    <td>${duplicates.toDouble / (total - secondary) * 100}%</td>
                 </tr>
             #end
         #end

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py → bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py

@@ -9,8 +9,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala → bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */
@@ -17,15 +16,16 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort }
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
-import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.intervals.BedCheck
 import org.broadinstitute.gatk.queue.QScript
 
 class BamMetrics(val root: Configurable) extends QScript
@@ -41,6 +41,8 @@ class BamMetrics(val root: Configurable) extends QScript
   @Input(doc = "Bam File", shortName = "BAM", required = true)
   var inputBam: File = _
 
+  override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
+
   /** return location of summary file */
   def summaryFile = (sampleId, libId) match {
     case (Some(s), Some(l)) => new File(outputDir, s + "-" + l + ".BamMetrics.summary.json")
@@ -72,6 +74,8 @@ class BamMetrics(val root: Configurable) extends QScript
   /** executed before script */
   def init(): Unit = {
     inputFiles :+= new InputFile(inputBam)
+    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
+    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
   }
 
   /** Script to add jobs */
@@ -162,7 +166,11 @@ class BamMetrics(val root: Configurable) extends QScript
       addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
       add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
 
-      val bedCov = BedtoolsCoverage(this, intervals.bed, inputBam, depth = true)
+      val sorter = new BedtoolsSort(this)
+      sorter.input = intervals.bed
+      sorter.output = swapExt(targetDir, intervals.bed, ".bed", ".sorted.bed")
+      add(sorter)
+      val bedCov = BedtoolsCoverage(this, sorter.output, inputBam, depth = true)
       val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       covStats.title = Some("Coverage Plot")
       covStats.subTitle = Some(s"for file '$targetName.bed'")

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala → bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */
@@ -98,6 +97,7 @@ 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
@@ -126,9 +126,9 @@ object BammetricsReport extends ReportBuilder {
         summary, Some(sample), lib).value.getOrElse(0).toString.toLong
       val sb = new StringBuffer()
       if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
-      sb.append((mapped - duplicates) + "\t")
+      sb.append((mapped - duplicates - secondary) + "\t")
       sb.append(duplicates + "\t")
-      sb.append((total - mapped - secondary) + "\t")
+      sb.append((total - mapped) + "\t")
       sb.append(secondary)
       sb.toString
     }
@@ -161,6 +161,7 @@ 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
@@ -249,6 +250,7 @@ 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
@@ -339,6 +341,7 @@ 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

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala → bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala → bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

public/bammetrics/src/test/resources/log4j.properties → bammetrics/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala → bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */
@@ -37,7 +36,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
 
   def initPipeline(map: Map[String, Any]): BamMetrics = {
     new BamMetrics() {
-      override def configName = "bammetrics"
+      override def configNamespace = "bammetrics"
       override def globalConfig = new Config(map)
       qSettings = new QSettings
       qSettings.runName = "test"
@@ -61,9 +60,9 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
       Map(BamMetricsTest.executables.toSeq: _*)) ++
-      (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
+      (if (amplicon) Map("amplicon_bed" -> BamMetricsTest.ampliconBed.getAbsolutePath) else Map()) ++
       (if (rna) Map("annotation_refflat" -> "transcripts.refFlat") else Map()) ++
-      Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
+      Map("regions_of_interest" -> (1 to rois).map(BamMetricsTest.roi(_).getAbsolutePath).toList)
     val bammetrics: BamMetrics = initPipeline(map)
 
     bammetrics.inputBam = BamMetricsTest.bam
@@ -94,6 +93,14 @@ object BamMetricsTest {
 
   val bam = new File(outputDir, "input" + File.separator + "bla.bam")
   Files.touch(bam)
+  val ampliconBed = new File(outputDir, "input" + File.separator + "amplicon_bed.bed")
+  Files.touch(ampliconBed)
+
+  def roi(i: Int): File = {
+    val roi = new File(outputDir, "input" + File.separator + s"roi${i}.bed")
+    Files.touch(roi)
+    roi
+  }
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)

public/basty/pom.xml → basty/pom.xml

@@ -9,8 +9,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 
@@ -32,7 +31,7 @@
     <parent>
         <groupId>nl.lumc.sasc</groupId>
         <artifactId>Biopet</artifactId>
-        <version>0.6.0</version>
+        <version>0.7.0</version>
         <relativePath>../</relativePath>
     </parent>
     

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala → basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */
@@ -22,26 +21,28 @@ package nl.lumc.sasc.biopet.pipelines.basty
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
+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
 import org.broadinstitute.gatk.queue.QScript
 
-trait BastyTrait extends MultiSampleQScript {
-  qscript: QScript =>
+class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
+  qscript =>
+
+  def this() = this(null)
 
   case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
 
-  def variantcallers = List("freebayes")
+  def variantcallers = List("unifiedgenotyper")
 
   override def defaults = Map(
     "ploidy" -> 1,
     "variantcallers" -> variantcallers
   )
 
-  lazy val shiva: ShivaTrait = new Shiva(qscript)
+  lazy val shiva = new Shiva(qscript)
 
   def summaryFile: File = new File(outputDir, "Basty.summary.json")
 
@@ -131,11 +132,11 @@ trait BastyTrait extends MultiSampleQScript {
       raxmlMl.p = Some(seed)
       raxmlMl.n = outputName + "_ml"
       raxmlMl.w = dirSufixRaxml
-      raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
+      raxmlMl.N = config("ml_runs", default = 20, namespace = "raxml")
       add(raxmlMl)
 
       val r = new scala.util.Random(seed)
-      val numBoot = config("boot_runs", default = 100, submodule = "raxml").asInt
+      val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
       val bootList = for (t <- 0 until numBoot) yield {
         val raxmlBoot = new Raxml(this)
         raxmlBoot.input = variants
@@ -194,3 +195,5 @@ trait BastyTrait extends MultiSampleQScript {
     FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
   }
 }
+
+object Basty extends PipelineCommand

public/basty/src/test/resources/log4j.properties → basty/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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-aggregate/pom.xml

 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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