Adding toucan pipeline stub

protected/biopet-protected-package/BiopetProtectedPackage.iml

@@ -95,6 +95,7 @@
     <orderEntry type="module" module-name="Gentrap" />
     <orderEntry type="module" module-name="Sage" />
     <orderEntry type="module" module-name="Yamsvp" />
+    <orderEntry type="module" module-name="Toucan" />
     <orderEntry type="module" module-name="BiopetGatkPipelines" />
     <orderEntry type="module" module-name="BiopetGatkExtensions" />
     <orderEntry type="module" module-name="Basty" />

public/biopet-framework/BiopetFramework.iml

@@ -5,8 +5,8 @@
     <output-test url="file://$MODULE_DIR$/target/test-classes" />
     <content url="file://$MODULE_DIR$">
       <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
       <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
       <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
       <excludeFolder url="file://$MODULE_DIR$/target" />
     </content>

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

+package nl.lumc.sasc.biopet.extensions
+
+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.{ Output, Input }
+
+/**
+ * Created by ahbbollen on 15-1-15.
+ */
+class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
+
+  executable = config("exe", submodule = "perl", default = "perl")
+  var vep_script: String = config("vep_script", required = true)
+
+  @Input(doc = "input VCF", required = true)
+  var input: File = _
+
+  @Output(doc = "output file", required = true)
+  var output: File = _
+
+  override val versionRegex = """version (\d*)""".r
+  override def versionCommand = executable + " " + vep_script + " --help"
+
+  //Boolean vars
+  var v: Boolean = config("v")
+  var q: Boolean = config("q")
+  var no_progress: Boolean = config("no_progress")
+  var everything: Boolean = config("everything")
+  var force: Boolean = config("force")
+  var no_stats: Boolean = config("no_stats")
+  var stats_text: Boolean = config("stats_text")
+  var html: Boolean = config("html")
+  var cache: Boolean = config("cache")
+  var humdiv: Boolean = config("humdiv")
+  var regulatory: Boolean = config("regulatory")
+  var cell_type: Boolean = config("cell_type")
+  var phased: Boolean = config("phased")
+  var allele_number: Boolean = config("allele_number")
+  var numbers: Boolean = config("numbers")
+  var domains: Boolean = config("domains")
+  var no_escape: Boolean = config("no_escape")
+  var hgvs: Boolean = config("hgvs")
+  var protein: Boolean = config("protein")
+  var symbol: Boolean = config("symbol")
+  var ccds: Boolean = config("ccds")
+  var uniprot: Boolean = config("uniprot")
+  var tsl: Boolean = config("tsl")
+  var canonical: Boolean = config("canonical")
+  var biotype: Boolean = config("biotype")
+  var xref_refseq: Boolean = config("xref_refseq")
+  var check_existing: Boolean = config("check_existing")
+  var check_alleles: Boolean = config("check_alleles")
+  var check_svs: Boolean = config("svs")
+  var gmaf: Boolean = config("gmaf")
+  var maf_1kg: Boolean = config("maf_1kg")
+  var maf_esp: Boolean = config("maf_esp")
+  var old_map: Boolean = config("old_maf")
+  var pubmed: Boolean = config("pubmed")
+  var failed: Boolean = config("failed")
+  var vcf: Boolean = config("vcf", default = true)
+  var json: Boolean = config("json")
+  var gvf: Boolean = config("gvf")
+  var check_ref: Boolean = config("check_ref")
+  var coding_only: Boolean = config("coding_only")
+  var no_intergenic: Boolean = config("no_intergenic")
+  var pick: Boolean = config("pick")
+  var pick_allele: Boolean = config("pick_allele")
+  var flag_pick: Boolean = config("flag_pick")
+  var flag_pick_allele: Boolean = config("flag_pick_allele")
+  var per_gene: Boolean = config("per_gene")
+  var most_severe: Boolean = config("most_severe")
+  var summary: Boolean = config("summary")
+  var filter_common: Boolean = config("filter_common")
+  var check_frequency: Boolean = config("check_frequency")
+  var allow_non_variant: Boolean = config("allow_non_variant")
+  var database: Boolean = config("database")
+  var genomes: Boolean = config("genomes")
+  var gencode_basic: Boolean = config("gencode_basic")
+  var refseq: Boolean = config("refseq")
+  var merged: Boolean = config("merged")
+  var all_refseq: Boolean = config("all_refseq")
+  var lrg: Boolean = config("lrg")
+  var no_whole_genome: Boolean = config("no_whole_genome")
+  var skip_db_check: Boolean = config("skip_db_check")
+
+  // Textual args
+  var vep_config: String = config("config")
+  var species: String = config("species")
+  var assembly: String = config("assembly")
+  var format: String = config("format")
+  var dir: String = config("dir")
+  var dir_cache: String = config("dir_cache")
+  var dir_plugins: String = config("dir_plugins")
+  var fasta: File = config("fasta")
+  var sift: String = config("sift")
+  var polyphen: String = config("polyphen")
+  var custom: String = config("custom")
+  var plugin: List[String] = config("plugin")
+  var individual: String = config("individual")
+  var fields: String = config("fields")
+  var convert: String = config("convert")
+  var terms: String = config("terms")
+  var chr: String = config("chr")
+  var pick_order: String = config("pick_order")
+  var freq_pop: String = config("check_pop")
+  var freq_gt_lt: String = config("freq_gt_lt")
+  var freq_filter: String = config("freq_filter")
+  var filter: String = config("filter")
+  var host: String = config("host")
+  var user: String = config("user")
+  var password: String = config("password")
+  var registry: String = config("registry")
+  var build: String = config("build")
+  var compress: String = config("compress")
+  var cache_region_size: String = config("cache_region_size")
+
+  // Numeric args
+  var fork: Option[Int] = config("fork")
+  var cache_version: Option[Int] = config("cache_version")
+  var freq_freq: Option[Float] = config("freq_freq")
+  var port: Option[Int] = config("port")
+  var db_version: Option[Int] = config("db_version")
+  var buffer_size: Option[Int] = config("buffer_size")
+
+  def cmdLine = required(executable) +
+    required(vep_script) +
+    required("-i", input) +
+    required("-o", output) +
+    conditional(v, "-v") +
+    conditional(q, "-q") +
+    conditional(no_progress, "--no_progress") +
+    conditional(everything, "--everything") +
+    conditional(force, "--force_overwrite") +
+    conditional(no_stats, "--no_stats") +
+    conditional(stats_text, "--stats_text") +
+    conditional(html, "--html") +
+    conditional(cache, "--cache") +
+    conditional(humdiv, "--humdiv") +
+    conditional(regulatory, "--regulatory") +
+    conditional(cell_type, "--cel_type") +
+    conditional(phased, "--phased") +
+    conditional(allele_number, "--allele_number") +
+    conditional(numbers, "--numbers") +
+    conditional(domains, "--domains") +
+    conditional(no_escape, "--no_escape") +
+    conditional(hgvs, "--hgvs") +
+    conditional(protein, "--protein") +
+    conditional(symbol, "--symbol") +
+    conditional(ccds, "--ccds") +
+    conditional(uniprot, "--uniprot") +
+    conditional(tsl, "--tsl") +
+    conditional(canonical, "--canonical") +
+    conditional(biotype, "--biotype") +
+    conditional(xref_refseq, "--xref_refseq") +
+    conditional(check_existing, "--check_existing") +
+    conditional(check_alleles, "--check_alleles") +
+    conditional(check_svs, "--check_svs") +
+    conditional(gmaf, "--gmaf") +
+    conditional(maf_1kg, "--maf_1kg") +
+    conditional(maf_esp, "--maf_esp") +
+    conditional(pubmed, "--pubmed") +
+    conditional(failed, "--failed") +
+    conditional(vcf, "--vcf") +
+    conditional(json, "--json") +
+    conditional(gvf, "--gvf") +
+    conditional(check_ref, "--check_ref") +
+    conditional(coding_only, "--coding_only") +
+    conditional(no_intergenic, "--no_intergenic") +
+    conditional(pick, "--pick") +
+    conditional(pick_allele, "--pick_allele") +
+    conditional(flag_pick, "--flag_pick") +
+    conditional(flag_pick_allele, "--flag_pick_allele") +
+    conditional(per_gene, "--per_gene") +
+    conditional(most_severe, "--most_severe") +
+    conditional(summary, "--summary") +
+    conditional(filter_common, "--filter_common") +
+    conditional(check_frequency, "--check_frequency") +
+    conditional(allow_non_variant, "--allow_non_variant") +
+    conditional(database, "--database") +
+    conditional(genomes, "--genomes") +
+    conditional(gencode_basic, "--gencode_basic") +
+    conditional(refseq, "--refseq") +
+    conditional(merged, "--merged") +
+    conditional(all_refseq, "--all_refseq") +
+    conditional(lrg, "--lrg") +
+    conditional(no_whole_genome, "--no_whole_genome") +
+    conditional(skip_db_check, "--skip_db_check") +
+    optional("--config", vep_config) +
+    optional("--species", species) +
+    optional("--assembly", assembly) +
+    optional("--format", format) +
+    optional("--dir", dir) +
+    optional("--dir_cache", dir_cache) +
+    optional("--dir_plugins", dir_plugins) +
+    optional("--fasta", fasta) +
+    optional("--sift", sift) +
+    optional("--polyphen", polyphen) +
+    optional("--custom", custom) +
+    repeat("--plugin", plugin) +
+    optional("--individual", individual) +
+    optional("--fields", fields) +
+    optional("--convert", convert) +
+    optional("--terms", terms) +
+    optional("--chr", chr) +
+    optional("--pick_order", pick_order) +
+    optional("--freq_pop", freq_pop) +
+    optional("--freq_gt_lt", freq_gt_lt) +
+    optional("--freq_filter", freq_filter) +
+    optional("--filter", filter) +
+    optional("--host", host) +
+    optional("--user", user) +
+    optional("--password", password) +
+    optional("--registry", registry) +
+    optional("--build", build) +
+    optional("--compress", compress) +
+    optional("--cache_region_size", cache_region_size) +
+    optional("--fork", fork) +
+    optional("--cache_version", cache_version) +
+    optional("--freq_freq", freq_freq) +
+    optional("--port", port) +
+    optional("--db_version", db_version) +
+    optional("--buffer_size", buffer_size)
+
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala

@@ -25,12 +25,17 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
   javaMainClass = getClass.getName
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
-  var InputVCF: File = _
-
-  //TODO: Add flags?
+  var inputVCF: File = _
 
   @Output(doc = "Output VCF", shortName = "OutputFile", required = true)
-  var OutputVCF: File = _
+  var outputVCF: File = _
+
+  var mode: String = config("mode", default = "explode")
+
+  override def commandLine = super.commandLine +
+    required("-I", inputVCF) +
+    required("-O", outputVCF) +
+    required("-m", mode)
 }
 
 object VEPNormalizer extends ToolCommand {
@@ -280,7 +285,7 @@ object VEPNormalizer extends ToolCommand {
 
   case class Args(inputVCF: File = null,
                   outputVCF: File = null,
-                  mode: String = "standard") extends AbstractArgs
+                  mode: String = null) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
 

public/biopet-public-package/BiopetPublicPackage.iml

@@ -94,5 +94,6 @@
     <orderEntry type="module" module-name="Gentrap" />
     <orderEntry type="module" module-name="Sage" />
     <orderEntry type="module" module-name="Yamsvp" />
+    <orderEntry type="module" module-name="Toucan" />
   </component>
 </module>
\ No newline at end of file

public/biopet-public-package/pom.xml

@@ -75,6 +75,11 @@
             <artifactId>Yamsvp</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Toucan</artifactId>
+            <version>${project.version}</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

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

@@ -22,7 +22,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
     nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
     nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
-    nl.lumc.sasc.biopet.pipelines.sage.Sage
+    nl.lumc.sasc.biopet.pipelines.sage.Sage,
+    nl.lumc.sasc.biopet.pipelines.toucan.Toucan
   )
 
   def tools: List[MainCommand] = List(

public/pom.xml

@@ -33,6 +33,7 @@
         <module>mapping</module>
         <module>sage</module>
         <module>yamsvp</module>
+        <module>toucan</module>
     </modules>
     
     <properties>

public/toucan/.gitignore

+/target/
\ No newline at end of file

public/toucan/Flexiprep.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="BiopetFramework" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
+    <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
+    <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+    <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools:1.4.2">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
+    <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
+    <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
+    <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
+    <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
+    <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools.jar:1.5">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
+    <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
+    <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
+    <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
+    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
+    <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
+    <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
+    <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
+    <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+    <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+    <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+  </component>
+</module>
\ No newline at end of file

public/toucan/pom.xml

+<!--
+
+    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">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>Toucan</artifactId>
+    <packaging>jar</packaging>
+    
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.3.0-DEV</version>
+        <relativePath>../</relativePath>
+    </parent>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>Toucan</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+</project>

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

+package nl.lumc.sasc.biopet.pipelines.toucan
+
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
+import nl.lumc.sasc.biopet.tools.VEPNormalizer
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
+/**
+ * Created by ahbbollen on 15-1-15.
+ */
+class Toucan(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Input VCF file", shortName = "Input", required = true)
+  var inputVCF: File = _
+
+  def init(): Unit = {
+
+  }
+
+  defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
+
+  def biopetScript(): Unit = {
+    val vep = new VariantEffectPredictor(this)
+    vep.input = inputVCF
+    vep.output = outputDir + inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf"
+    vep.isIntermediate = true
+    add(vep)
+
+    val normalizer = new VEPNormalizer(this)
+    normalizer.inputVCF = vep.output
+    normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
+    add(normalizer)
+  }
+
+}
+
+object Toucan extends PipelineCommand
\ No newline at end of file