Merge branch 'feature-gears' into 'develop'

Feature gears (metagenomics)

Metagenomics pipeline, start from bam or from FastQ files.

Dependencies:
- Sambamba (v0.5.1+)
- Kraken

See merge request !168

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.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 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.kraken
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.util.matching.Regex
+
+/** Extension for Kraken */
+class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
+
+  @Input(doc = "Input: FastQ or FastA")
+  var input: List[File] = _
+
+  var db: File = config("db")
+
+  var inputFastQ: Boolean = true
+  var compression: Boolean = false
+  var compressionGzip: Boolean = false
+  var compressionBzip: Boolean = false
+
+  var quick: Boolean = false
+  var min_hits: Option[Int] = config("min_hits")
+
+  @Output(doc = "Unidentified reads", required = false)
+  var unclassified_out: Option[File] = None
+  @Output(doc = "Identified reads", required = false)
+  var classified_out: Option[File] = None
+
+  @Output(doc = "Output with hits per sequence")
+  var output: File = _
+  var preload: Boolean = config("preload", default = true)
+  var paired: Boolean = config("paired", default = false)
+
+  executable = config("exe", default = "kraken")
+  override val versionRegex = """Kraken version ([\d\w\-\.]+)\n.*""".r
+  override val versionExitcode = List(0, 1)
+
+  override val defaultCoreMemory = 8.0
+  override val defaultThreads = 4
+
+  override def versionCommand = executable + " --version"
+
+  /** Sets readgroup when not set yet */
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+  }
+
+  /** Returns command to execute */
+  def cmdLine = {
+    var cmd: String = required(executable) +
+      "--db" + required(db) +
+      optional("--threads", nCoresRequest) +
+      conditional(inputFastQ, "--fastq-input") +
+      conditional(inputFastQ == false, "--fasta-input") +
+      conditional(quick, "--quick")
+
+    min_hits match {
+      case Some(v) => cmd += "--min_hits " + v
+      case _       => cmd += ""
+    }
+
+    cmd += optional("--unclassified-out ", unclassified_out.get) +
+      optional("--classified-out ", classified_out.get) +
+      "--output" + required(output) +
+      conditional(preload, "--preload") +
+      conditional(paired, "--paired")
+
+    // finally the input files (R1 [R2])
+    cmd += input.mkString(" ")
+
+    cmd
+  }
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.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 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.kraken
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/** Extension for Kraken */
+class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction {
+
+  executable = config("exe", default = "kraken-report")
+  override val versionRegex = """Kraken version (.*)""".r
+  override val versionExitcode = List(0, 1)
+
+  override val defaultCoreMemory = 4.0
+  override val defaultThreads = 1
+
+  override def versionCommand = new File(new File(executable).getParent, "kraken").getAbsolutePath + " --version"
+
+  var db: File = config("db")
+  var show_zeros: Boolean = config("show_zeros", default = false)
+
+  @Input(doc = "Input raw kraken analysis")
+  var input: File = _
+
+  @Output(doc = "Output path kraken report")
+  var output: File = _
+
+  def cmdLine: String = {
+    val cmd: String = "--db " + required(db) +
+      conditional(show_zeros, "--show-zeros") +
+      input.getAbsolutePath + ">" + output.getAbsolutePath
+    cmd
+  }
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.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 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.sambamba
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import java.io.File
+
+/** Extension for sambamba flagstat  */
+class SambambaView(val root: Configurable) extends Sambamba {
+  override val defaultThreads = 2
+
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Output(doc = "output File")
+  var output: File = _
+
+  var filter: Option[String] = _
+  val format: Option[String] = config("format", default = "bam")
+  val regions: Option[File] = config("regions")
+  val compression_level: Option[Int] = config("compression_level", default = 6)
+
+  /** Returns command to execute */
+  def cmdLine = required(executable) +
+    required("view") +
+    optional("--filter", filter) +
+    optional("--nthreads", nCoresRequest) +
+    optional("--format", format.get) +
+    optional("--regions", regions) +
+    optional("--compression-level", compression_level) +
+    required("--output" + output) +
+    required(input)
+}

public/biopet-public-package/pom.xml

@@ -80,6 +80,11 @@
             <artifactId>Kopisu</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Gears</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Bam2Wig</artifactId>

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

@@ -30,7 +30,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
   def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
-    nl.lumc.sasc.biopet.pipelines.basty.Basty
+    nl.lumc.sasc.biopet.pipelines.basty.Basty,
+    nl.lumc.sasc.biopet.pipelines.gears.Gears
   ) ::: protectedPipelines
 
   def tools: List[MainCommand] = List(

public/gears/.gitignore

+target

public/gears/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 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.
+
+-->
+<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">
+    <parent>
+        <artifactId>Biopet</artifactId>
+        <groupId>nl.lumc.sasc</groupId>
+        <version>0.4.0-DEV</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <inceptionYear>2015</inceptionYear>
+    <artifactId>Gears</artifactId>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Mapping</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.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 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.pipelines.gears
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import org.broadinstitute.gatk.queue.QScript
+
+class Gears(val root: Configurable) extends QScript with GearsTrait {
+  def this() = this(null)
+}
+
+/** This object give a default main method to the pipelines */
+object Gears extends PipelineCommand
\ No newline at end of file

public/gears/src/test/resources/log4j.properties

+#
+# 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.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file

public/pom.xml

@@ -34,6 +34,7 @@
         <module>sage</module>
         <module>kopisu</module>
         <module>yamsvp</module>
+        <module>gears</module>
         <module>bam2wig</module>
         <module>carp</module>
 	    <module>toucan</module>
@@ -202,6 +203,7 @@
                       <exclude>**/*.bed</exclude>
                       <exclude>**/*.refFlat</exclude>
                       <exclude>**/*.R</exclude>
+                      <exclude>**/*.rscript</exclude>
                   </excludes>
               </configuration>
           </plugin>