diff --git a/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
new file mode 100644
index 0000000000000000000000000000000000000000..3cbaf06412488bece8e795ef097c2582130920a3
--- /dev/null
+++ b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+#
+# 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.
+#
+
+
+from __future__ import print_function
+
+__author__="Wai Yi Leung"
+
+import sys
+
+if __name__ == "__main__":
+ """
+ Fix the mpileupformat for RNA mpileup
+ Solution offered by Irina Pulyakhina (LUMC-HG)
+ http://www.biostars.org/p/78542/
+ """
+ for line in sys.stdin:
+ l = line.strip().split("\t")
+ if l[3] == "0":
+ # no alignment to this position
+ print("\t".join(map(str, l)))
+ continue
+
+ fix_col = l[4].replace('<', '').replace('>', '')
+
+ new_size = len(fix_col)
+ old_size = len(l[4])
+ if new_size != old_size:
+ l[4] = fix_col
+ l[3] = "{}".format(new_size)
+
+ if new_size == 0:
+ l[5] = ""
+
+ print("\t".join(map(str, l)))
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
index 321cb8b9c5960936da9d8f5bcac0d2fdb9937627..a43fc4734852642b92e7924e2209073616197f6c 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
@@ -36,5 +36,5 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
def cmdLine = required(executable) +
conditional(f, "-f") +
" -c " + repeat(input) +
- " > " + required(output)
+ (if (outputAsStsout) "" else " > " + required(output))
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
new file mode 100644
index 0000000000000000000000000000000000000000..827da73e3779003746a8ec16044c7726faa03337
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
@@ -0,0 +1,12 @@
+package nl.lumc.sasc.biopet.extensions.varscan
+
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by sajvanderzeeuw on 19-1-16.
+ */
+class FixMpileup(val root: Configurable) extends PythonCommandLineFunction {
+ setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/extensions/varscan/")
+ def cmdLine = getPythonCommand
+}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
index 76da0423cea32f599c978e852ca0aa35a740137e..67d3d34ee7be4dbd7e77fe030ee9914674522348 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
@@ -23,7 +23,7 @@ abstract class Varscan extends BiopetJavaCommandLineFunction with Version {
jarFile = config("varscan_jar")
- def versionCommand = super.commandLine
+ def versionCommand = s"$executable -jar $jarFile"
def versionRegex = """VarScan v(.*)""".r
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
similarity index 75%
rename from public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
index 4fb0a05fd7e04617c15a68c63763d7e60da322d4..085b1bc37031fbf1ef99bd8448dbcba6fc0d07a8 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
@@ -20,7 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-class Mpileup2cns(val root: Configurable) extends Varscan {
+class VarscanMpileup2cns(val root: Configurable) extends Varscan {
@Input(doc = "Input mpileup file", required = false) // if not defined, input is stdin
var input: Option[File] = None
@@ -49,22 +49,17 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
variants.foreach { case v => require(validValues.contains(v), "variants value must be either 0 or 1") }
}
- override def cmdLine = {
- val baseCommand = super.cmdLine + required("mpileup2cns") +
- required("", input) +
- required("--min-coverage", minCoverage) +
- required("--min-reads2", minReads2) +
- required("--min-avg-qual", minAvgQual) +
- required("--min-var-freq", minVarFreq) +
- required("--min-freq-for-hom", minFreqForHom) +
- required("--p-value", pValue) +
- required("--strand-filter", strandFilter) +
- required("--output-vcf", outputVcf) +
- required("--vcf-sample-list", vcfSampleList) +
- required("--variants", variants)
-
- if (output.isDefined) baseCommand + " > " + required(output)
- else baseCommand
- }
-
+ override def cmdLine = super.cmdLine + required("mpileup2cns") +
+ required(input) +
+ optional("--min-coverage", minCoverage) +
+ optional("--min-reads2", minReads2) +
+ optional("--min-avg-qual", minAvgQual) +
+ optional("--min-var-freq", minVarFreq) +
+ optional("--min-freq-for-hom", minFreqForHom) +
+ optional("--p-value", pValue) +
+ optional("--strand-filter", strandFilter) +
+ optional("--output-vcf", outputVcf) +
+ optional("--vcf-sample-list", vcfSampleList) +
+ optional("--variants", variants) +
+ (if (outputAsStsout) "" else " > " + required(output))
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index f2f11a03e775ebe5a7fa4161813a0157c8f7976a..2d1f270c680338c099baf27c6325551d8f0dd590 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.varscan.Mpileup2cns
+import nl.lumc.sasc.biopet.extensions.varscan.VarscanMpileup2cns
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -65,7 +65,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction wi
override def cmdLine: String = required(executable) + required("-vP") + required("""\t\t""")
}
- private val varscan = new Mpileup2cns(wrapper.root) {
+ private val varscan = new VarscanMpileup2cns(wrapper.root) {
override def configName = wrapper.configName
strandFilter = Option(0)
outputVcf = Option(1)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
index 2ace6f962b245acca0e65212ea6ee11bb478ebf0..4207bf0a358393df51037fdc644bd9c00578c947 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
@@ -28,6 +28,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
+ val flexiprepExecuted = summary.getLibraryValues("flexiprep")
+ .exists { case ((sample, lib), value) => value.isDefined }
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
@@ -51,25 +53,35 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
(if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
- List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+ (if (flexiprepExecuted) List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
- ),
+ )
+ else Nil),
pageArgs
)
}
/** Files page, can be used general or at sample level */
- def filesPage: ReportPage = ReportPage(List(), List(
- "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
- "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
- "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
- "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
- Map("pipelineName" -> pipelineName, "fileTag" -> "output_bam_preprocess"))), Map())
+ def filesPage: ReportPage = {
+ val flexiprepExecuted = summary.getLibraryValues("flexiprep")
+ .exists { case ((sample, lib), value) => value.isDefined }
+
+ ReportPage(List(), (if (flexiprepExecuted) List(
+ "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
+ "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"))
+ else Nil) :::
+ List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
+ "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
+ Map("pipelineName" -> pipelineName, "fileTag" -> "output_bam_preprocess"))), Map())
+ }
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+ val flexiprepExecuted = summary.getLibraryValues("flexiprep")
+ .exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
+
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
@@ -78,20 +90,23 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
"Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true))) ++
- List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ (if (flexiprepExecuted) List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
+ )
+ else Nil), args)
}
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
- "QC" -> FlexiprepReport.flexiprepPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
+ val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
+
+ ReportPage(
+ ("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
+ (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil),
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
+ (if (flexiprepExecuted) List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"))
+ else Nil),
+ args)
}
}
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index 31ba0a53f0fc034b406cca237656722ca9de9d6f..f08b4cc18402e995375f14f1095e922883b8dc98 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -156,7 +156,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript
}
/** Will generate all available variantcallers */
- protected def callersList: List[Variantcaller] = List(new Freebayes(this), new RawVcf(this), new Bcftools(this), new BcftoolsSingleSample(this))
+ protected def callersList: List[Variantcaller] = List(
+ new Freebayes(this),
+ new RawVcf(this),
+ new Bcftools(this),
+ new BcftoolsSingleSample(this),
+ new VarscanCnsSingleSample(this))
/** Location of summary file */
def summaryFile = new File(outputDir, "ShivaVariantcalling.summary.json")
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
new file mode 100644
index 0000000000000000000000000000000000000000..157013e5bbd0f22c8d74bf04355872f4bdb6cfaa
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -0,0 +1,61 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.PrintWriter
+
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.extensions.varscan.{ FixMpileup, VarscanMpileup2cns }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by sajvanderzeeuw on 15-1-16.
+ */
+class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
+ val name = "varscan_cns_singlesample"
+ protected def defaultPrio = 25
+
+ override def defaults = Map(
+ "samtoolsmpileup" -> Map(
+ "disable_baq" -> true,
+ "depth" -> 1000000
+ ),
+ "varscanmpileup2cns" -> Map("strand_filter" -> 0)
+ )
+
+ override def fixedValues = Map(
+ "samtoolsmpileup" -> Map("output_mapping_quality" -> true),
+ "varscanmpileup2cns" -> Map("output_vcf" -> 1)
+ )
+
+ def biopetScript: Unit = {
+ val sampleVcfs = for ((sample, inputBam) <- inputBams.toList) yield {
+ val mpileup = new SamtoolsMpileup(this)
+ mpileup.input = List(inputBam)
+
+ val sampleVcf = new File(outputDir, s"${name}_$sample.vcf.gz")
+
+ val sampleFile = new File(outputDir, s"$sample.name.txt")
+ sampleFile.getParentFile.mkdirs()
+ sampleFile.deleteOnExit()
+ val writer = new PrintWriter(sampleFile)
+ writer.println(sample)
+ writer.close()
+
+ val varscan = new VarscanMpileup2cns(this)
+ varscan.vcfSampleList = Some(sampleFile)
+
+ add(mpileup | new FixMpileup(this) | varscan | new Bgzip(this) > sampleVcf)
+ add(Tabix(this, sampleVcf))
+
+ sampleVcf
+ }
+
+ val cv = new CombineVariants(this)
+ cv.inputFiles = sampleVcfs
+ cv.outputFile = outputFile
+ cv.setKey = "null"
+ cv.excludeNonVariants = true
+ add(cv)
+ }
+}
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 94edda97a3e893ab8bba6d4016f003c2b0242b57..dda3fb8c166cfcfbcc883d8c289cf172207a8964 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
@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams <- 0 to 3;
raw <- bool;
bcftools <- bool;
- bcftools_singlesample <- bool;
- freebayes <- bool
- ) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
+ bcftoolsSinglesample <- bool;
+ freebayes <- bool;
+ varscanCnsSinglesample <- bool
+ ) yield Array(bams, raw, bcftools, bcftoolsSinglesample, freebayes, varscanCnsSinglesample)).toArray
}
@Test(dataProvider = "shivaVariantcallingOptions")
def testShivaVariantcalling(bams: Int,
raw: Boolean,
bcftools: Boolean,
- bcftools_singlesample: Boolean,
- freebayes: Boolean) = {
+ bcftoolsSinglesample: Boolean,
+ freebayes: Boolean,
+ varscanCnsSinglesample: Boolean) = {
val callers: ListBuffer[String] = ListBuffer()
if (raw) callers.append("raw")
if (bcftools) callers.append("bcftools")
- if (bcftools_singlesample) callers.append("bcftools_singlesample")
+ if (bcftoolsSinglesample) callers.append("bcftools_singlesample")
if (freebayes) callers.append("freebayes")
+ if (varscanCnsSinglesample) callers.append("varscan_cns_singlesample")
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
- val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftools_singlesample && !freebayes)
+ val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes && !varscanCnsSinglesample)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
@@ -83,7 +86,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
if (!illegalArgumentException) {
pipeline.script()
- pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+ pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe (1 + (if (raw) 1 else 0) + (if (varscanCnsSinglesample) 1 else 0))
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
@@ -130,6 +133,7 @@ object ShivaVariantcallingTest {
"freebayes" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test"),
"bgzip" -> Map("exe" -> "test"),
- "tabix" -> Map("exe" -> "test")
+ "tabix" -> Map("exe" -> "test"),
+ "varscan_jar" -> "test"
)
}
\ No newline at end of file