diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index f8d94cd6a31db716cf1164faacfa6127ecae8cd7..634a3fb17945144093f26dbcd11427b65474f7b6 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -107,6 +107,9 @@ object ShivaTest {
val config = Map(
"name_prefix" -> "test",
+ "cache" -> true,
+ "dir" -> "test",
+ "vep_script" -> "test",
"output_dir" -> outputDir,
"reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 8ebb3d95266da636fc4ef63712d5d35496b9ecaa..1609f5c31bb4a6b648a9a5aa4bb5a7de531e4714 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -122,6 +122,9 @@ object ShivaVariantcallingTest {
val config = Map(
"name_prefix" -> "test",
"output_dir" -> outputDir,
+ "cache" -> true,
+ "dir" -> "test",
+ "vep_script" -> "test",
"reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 1adfd543149fbb8648a9d561e04fbf13f33e32f9..b124a08aa5944beebff8507c09646618c4bc0ab7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference {
executable = config("exe", submodule = "perl", default = "perl")
- var vep_script: String = config("vep_script")
+ var vepScript: String = config("vep_script")
@Input(doc = "input VCF", required = true)
var input: File = null
@@ -37,14 +37,14 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var output: File = null
override def versionRegex = """version (\d*)""".r
- override def versionCommand = executable + " " + vep_script + " --help"
+ override def versionCommand = executable + " " + vepScript + " --help"
//Boolean vars
var v: Boolean = config("v", default = true)
var q: Boolean = config("q", default = false)
var offline: Boolean = config("offline", default = false)
var no_progress: Boolean = config("no_progress", default = false)
- var everything: Boolean = config("everything", default = true)
+ var everything: Boolean = config("everything", default = false)
var force: Boolean = config("force", default = false)
var no_stats: Boolean = config("no_stats", default = false)
var stats_text: Boolean = config("stats_text", default = false)
@@ -144,15 +144,15 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override def beforeGraph(): Unit = {
super.beforeGraph()
if (!cache && !database) {
- throw new IllegalArgumentException("Must supply either cache or database")
+ throw new IllegalArgumentException("Must supply either cache or database for VariantEffectPredictor")
} else if (cache && dir.isEmpty) {
- throw new IllegalArgumentException("Must supply dir to cache")
+ throw new IllegalArgumentException("Must supply dir to cache for VariantEffectPredictor")
}
}
/** Returns command to execute */
def cmdLine = required(executable) +
- required(vep_script) +
+ required(vepScript) +
required("-i", input) +
required("-o", output) +
conditional(v, "-v") +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 9009d2918574fdba847adcdd5000ac10bd5e6a2f..8bdf74983208d5b1d5c480f7c9cbf511ecd7a4e1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -20,10 +20,48 @@ import java.io.File
import htsjdk.variant.variantcontext.VariantContextBuilder
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
+/**
+ * Biopet extension for tool VcfWithVcf
+ */
+class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
+ javaMainClass = getClass.getName
+
+ @Input(doc = "Input vcf file", shortName = "input", required = true)
+ var input: File = _
+
+ @Input(doc = "Secondary vcf file", shortName = "secondary", required = true)
+ var secondaryVcf: File = _
+
+ @Output(doc = "Output vcf file", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "Output vcf file index", shortName = "output", required = true)
+ private var outputIndex: File = _
+
+ var fields: List[(String, String, Option[String])] = List()
+
+ override def defaultCoreMemory = 2.0
+
+ override def beforeGraph() {
+ super.beforeGraph()
+ if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+ if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+ if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
+ }
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", output) +
+ required("-s", secondaryVcf) +
+ repeat("-f", fields.map(x => x._1 + ":" + x._2 + ":" + x._3.getOrElse("none")))
+}
+
/**
* This is a tool to annotate a vcf file with info value from a other vcf file
*
@@ -46,10 +84,10 @@ object VcfWithVcf extends ToolCommand {
opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
}
- opt[File]('O', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = x)
}
- opt[File]('S', "secondaryVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ opt[File]('s', "secondaryVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(secondaryVcf = x)
}
opt[String]('f', "field") unbounded () valueName "<field> or <input_field:output_field> or <input_field:output_field:method>" action { (x, c) =>
@@ -58,11 +96,11 @@ object VcfWithVcf extends ToolCommand {
else if (values.size > 1) c.copy(fields = Fields(values(0), values(1)) :: c.fields)
else c.copy(fields = Fields(x, x) :: c.fields)
} text """| If only <field> is given, the field's identifier in the output VCF will be identical to <field>.
- | By default we will return all values found for a given field.
- | With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
- | - max : takes maximum of found value, only works for numeric (integer/float) fields
- | - min : takes minemal of found value, only works for numeric (integer/float) fields
- | - unique: takes only unique values """.stripMargin
+ | By default we will return all values found for a given field.
+ | With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
+ | - max : takes maximum of found value, only works for numeric (integer/float) fields
+ | - min : takes minemal of found value, only works for numeric (integer/float) fields
+ | - unique: takes only unique values """.stripMargin
opt[Boolean]("match") valueName "<Boolean>" maxOccurs 1 action { (x, c) =>
c.copy(matchAllele = x)
} text "Match alternative alleles; default true"
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index 5878d03f32d5b9943bfb4e734b2c5f7d0b806a41..8543b7706670ef40d9a877f27a0bf1b1ed3d77a9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -45,7 +45,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
var inputVCF: File = null
@Output(doc = "Output VCF", shortName = "OutputFile", required = true)
- var outputVCF: File = null
+ var outputVcf: File = null
var mode: String = config("mode", default = "explode")
var doNotRemove: Boolean = config("donotremove", default = false)
@@ -54,7 +54,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
override def commandLine = super.commandLine +
required("-I", inputVCF) +
- required("-O", outputVCF) +
+ required("-O", outputVcf) +
required("-m", mode) +
conditional(doNotRemove, "--do-not-remove")
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index 4578e32298b66cb76ee6e3e8b422626e18e73c25..9996dfed3befed4e8913ee1377d04953607dfbc9 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -15,6 +15,7 @@
*/
package nl.lumc.sasc.biopet.tools
+import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
@@ -36,25 +37,25 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
Paths.get(getClass.getResource(p).toURI).toString
}
- val vepped_path = resourcePath("/VEP_oneline.vcf.gz")
- val unvepped_path = resourcePath("/unvepped.vcf.gz")
+ val veppedPath = resourcePath("/VEP_oneline.vcf.gz")
+ val unveppedPath = resourcePath("/unvepped.vcf.gz")
val rand = new Random()
@Test def testOutputTypeVcf() = {
- val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf"
- val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
- val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".vcf.gz"
- val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
main(arguments)
}
@Test def testOutputTypeBcf() = {
- val tmp_path = "/tmp/VcfWithVcf_" + rand.nextString(10) + ".bcf"
- val arguments = Array("-I", unvepped_path, "-S", vepped_path, "-O", tmp_path, "-f", "CSQ")
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
main(arguments)
}
diff --git a/public/shiva/pom.xml b/public/shiva/pom.xml
index e7d211a68363a3e8987d98938df3caa74c5abf65..36c227e8496da9a602bcdf4c60afe07880dc8af4 100644
--- a/public/shiva/pom.xml
+++ b/public/shiva/pom.xml
@@ -40,6 +40,11 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Toucan</artifactId>
+ <version>${project.version}</version>
+ </dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 5eb7bf4116c412729ecd4b943f6c3f5b9af62c5c..3f65bf2a20864e2017f512981daa0d37aca52772 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, SamToFastq }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import scala.collection.JavaConversions._
@@ -280,9 +281,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
} else None
lazy val svCalling = if (config("sv_calling", default = false).asBoolean) {
- val svCalling = new ShivaSvCalling(this)
- samples.foreach(x => x._2.preProcessBam.foreach(bam => svCalling.addBamFile(bam, Some(x._1))))
- Some(svCalling)
+ Some(new ShivaSvCalling(this))
} else None
/** This will add the mutisample variantcalling */
@@ -294,10 +293,21 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
vc.biopetScript()
addAll(vc.functions)
addSummaryQScript(vc)
+
+ if (config("annotation", default = true).asBoolean) {
+ val toucan = new Toucan(this)
+ toucan.outputDir = new File(outputDir, "annotation")
+ toucan.inputVCF = vc.finalFile
+ toucan.init()
+ toucan.biopetScript()
+ addAll(toucan.functions)
+ addSummaryQScript(toucan)
+ }
})
svCalling.foreach(sv => {
sv.outputDir = new File(outputDir, "sv_calling")
+ samples.foreach(x => x._2.preProcessBam.foreach(bam => sv.addBamFile(bam, Some(x._1))))
sv.init()
sv.biopetScript()
addAll(sv.functions)
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index d7e7eadf623a3271f6495d95f713b6725d6c1cff..e37756ef76504268f746dfb7ceda62cf29ed2d75 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -103,6 +103,9 @@ object ShivaTest {
val config = Map(
"name_prefix" -> "test",
"output_dir" -> outputDir,
+ "cache" -> true,
+ "dir" -> "test",
+ "vep_script" -> "test",
"reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index ed987ceaf4471a0659b627179a05781fa63b5b74..82e21f195aefde3199f19f5a5edf8088ea835201 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -103,6 +103,9 @@ object ShivaVariantcallingTest {
val config = Map(
"name_prefix" -> "test",
"output_dir" -> outputDir,
+ "cache" -> true,
+ "dir" -> "test",
+ "vep_script" -> "test",
"reference" -> (outputDir + File.separator + "ref.fa"),
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index ef59e2680a7093210a91e527c54545495d8a92f4..ccd47d551363be2bf65d0fd0176f02f8092060a1 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -16,9 +16,10 @@
package nl.lumc.sasc.biopet.pipelines.toucan
import nl.lumc.sasc.biopet.core.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.VepNormalizer
+import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
@@ -27,14 +28,13 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by ahbbollen on 15-1-15.
*/
-class Toucan(val root: Configurable) extends QScript with BiopetQScript with Reference {
+class Toucan(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript with Reference {
def this() = this(null)
@Input(doc = "Input VCF file", shortName = "Input", required = true)
var inputVCF: File = _
def init(): Unit = {
-
}
override def defaults = ConfigUtils.mergeMaps(Map(
@@ -52,10 +52,45 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Ref
val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output
- normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
+ normalizer.outputVcf = swapExt(outputDir, vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer)
+
+ // Optional annotation steps, depend is some files existing in the config
+ val gonlVcfFile: Option[File] = config("gonl_vcf")
+ val exacVcfFile: Option[File] = config("exac_vcf")
+
+ var outputFile = normalizer.outputVcf
+
+ gonlVcfFile match {
+ case Some(gonlFile) =>
+ val vcfWithVcf = new VcfWithVcf(this)
+ vcfWithVcf.input = outputFile
+ vcfWithVcf.secondaryVcf = gonlFile
+ vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
+ vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
+ add(vcfWithVcf)
+ outputFile = vcfWithVcf.output
+ case _ =>
+ }
+
+ exacVcfFile match {
+ case Some(exacFile) =>
+ val vcfWithVcf = new VcfWithVcf(this)
+ vcfWithVcf.input = outputFile
+ vcfWithVcf.secondaryVcf = exacFile
+ vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
+ vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
+ add(vcfWithVcf)
+ outputFile = vcfWithVcf.output
+ case _ =>
+ }
}
+ def summaryFile = new File(outputDir, "Toucan.summary.json")
+
+ def summaryFiles = Map()
+
+ def summarySettings = Map()
}
object Toucan extends PipelineCommand
\ No newline at end of file