diff --git a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
index f28b4d52f94b95ebece020fed591a2e4d8bbf806..a9ff3afa2daf3e3a1d48845b176fcc8489987b4d 100644
--- a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
@@ -31,6 +31,8 @@ class BiopetPipeline(val root: Configurable) extends QScript with SummaryQScript
// Executing a biopet pipeline inside
val shiva = new Shiva(this)
+ add(shiva)
+
shiva.init()
shiva.biopetScript()
addAll(shiva.functions)
diff --git a/protected/biopet-gatk-extensions/pom.xml b/protected/biopet-gatk-extensions/pom.xml
index 76da4b194ba8495a0fb3e84a81b29f2d1d37ffbd..bf0ce809bb4e3ff1178e4a95686e380c1f45b601 100644
--- a/protected/biopet-gatk-extensions/pom.xml
+++ b/protected/biopet-gatk-extensions/pom.xml
@@ -25,13 +25,13 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetCore</artifactId>
+ <artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-extensions-distribution</artifactId>
- <version>3.4</version>
+ <version>3.5</version>
</dependency>
</dependencies>
</project>
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
index e347ebf4743eca9b2f80bc3f072c922cb012e88a..60614ecc938bef58534c810423254fc56eab5dbc 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
@@ -8,8 +8,13 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Output
class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
+
+ @Output(required = false)
+ protected var vcfIndex: File = _
+
annotation ++= config("annotation", default = Seq(), freeVar = false).asStringList
if (config.contains("dbsnp")) dbsnp = config("dbsnp")
@@ -22,6 +27,11 @@ class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queu
stand_call_conf = config("stand_call_conf", default = 30)
stand_emit_conf = config("stand_emit_conf", default = 0)
}
+
+ override def freezeFieldValues(): Unit = {
+ super.freezeFieldValues()
+ if (out.getName.endsWith(".vcf.gz")) vcfIndex = new File(out.getAbsolutePath + ".tbi")
+ }
}
object GenotypeGVCFs {
@@ -29,6 +39,7 @@ object GenotypeGVCFs {
val gg = new GenotypeGVCFs(root)
gg.variant = gvcfFiles
gg.out = output
+ if (gg.out.getName.endsWith(".vcf.gz")) gg.vcfIndex = new File(gg.out.getAbsolutePath + ".tbi")
gg
}
}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
index 514879f9d2b96088a6e5b3e30eb969d44740934b..819a836bfe03486ca5b86a30708ead4bb9b39a67 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
@@ -5,11 +5,18 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
+import java.io.File
+
import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
+ @Gather(enabled = false)
+ @Output(required = false)
+ protected var vcfIndex: File = _
+
override val defaultThreads = 1
min_mapping_quality_score = config("minMappingQualityScore", default = 20)
@@ -40,6 +47,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
override def freezeFieldValues() {
super.freezeFieldValues()
+ if (out.getName.endsWith(".vcf.gz")) vcfIndex = new File(out.getAbsolutePath + ".tbi")
if (bamOutput != null && nct.getOrElse(1) > 1) {
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
nCoresRequest = Some(1)
@@ -47,10 +55,22 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
nct = Some(getThreads)
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
+}
+
+object HaplotypeCaller {
+ def apply(root: Configurable, inputFiles: List[File], outputFile: File): HaplotypeCaller = {
+ val hc = new HaplotypeCaller(root)
+ hc.input_file = inputFiles
+ hc.out = outputFile
+ if (hc.out.getName.endsWith(".vcf.gz")) hc.vcfIndex = new File(hc.out.getAbsolutePath + ".tbi")
+ hc
+ }
- def useGvcf() {
- emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
- variant_index_type = GATKVCFIndexType.LINEAR
- variant_index_parameter = config("variant_index_parameter", default = 128000)
+ def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
+ val hc = apply(root, List(inputFile), outputFile)
+ hc.emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
+ hc.variant_index_type = GATKVCFIndexType.LINEAR
+ hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
+ hc
}
-}
+}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
index 44a3eac6607a6165920ab4d4564c9777119a1ca9..32cf797a0f77d488a5aa0c7fda32fcfaa422e038 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
@@ -8,8 +8,12 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Output
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
+ @Output
+ protected var bamIndex: File = _
+
if (config.contains("scattercount")) scatterCount = config("scattercount")
}
@@ -19,6 +23,7 @@ object IndelRealigner {
ir.input_file :+= input
ir.targetIntervals = targetIntervals
ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
+ ir.bamIndex = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
ir
}
}
\ No newline at end of file
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
index 70d988f4b057572bc1c110ad597c232d6093a2cc..c0cecb873aceb39d8073e91bf7571a18f20f634d 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
@@ -5,9 +5,17 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
+import java.io.File
+
import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
+
+ @Gather(enabled = false)
+ @Output(required = false)
+ protected var vcfIndex: File = _
+
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
sample_ploidy = config("ploidy")
@@ -36,3 +44,14 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
}
}
+
+object UnifiedGenotyper {
+ def apply(root: Configurable, inputFiles: List[File], outputFile: File): UnifiedGenotyper = {
+ val ug = new UnifiedGenotyper(root)
+ ug.input_file = inputFiles
+ ug.out = outputFile
+ if (ug.out.getName.endsWith(".vcf.gz")) ug.vcfIndex = new File(ug.out.getAbsolutePath + ".tbi")
+ ug
+ }
+
+}
\ No newline at end of file
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
deleted file mode 100644
index e489c4afdf4a30b8ca0b2a965242eae7811ad24c..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+++ /dev/null
@@ -1,60 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-import scala.util.Random
-
-class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "Sample gvcf file")
- var sampleGvcf: File = _
-
- @Argument(doc = "SampleName", required = true)
- var sampleName: String = _
-
- @Input(doc = "Gvcf files", shortName = "I", required = false)
- var gvcfFiles: List[File] = Nil
-
- var reference: File = config("reference")
-
- @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = config("dbsnp")
-
- def init() {
- if (config.contains("gvcffiles")) for (file <- config("gvcffiles").asList)
- gvcfFiles ::= file.toString
- }
-
- def biopetScript() {
- var todoGvcfs = gvcfFiles
- var gvcfPool: List[File] = Nil
- addGenotypingPipeline(gvcfPool)
-
- while (todoGvcfs.nonEmpty) {
- val index = Random.nextInt(todoGvcfs.size)
- gvcfPool ::= todoGvcfs(index)
- addGenotypingPipeline(gvcfPool)
- todoGvcfs = todoGvcfs.filter(b => b != todoGvcfs(index))
- }
- }
-
- def addGenotypingPipeline(gvcfPool: List[File]) {
- val gatkGenotyping = new GatkGenotyping(this)
- gatkGenotyping.inputGvcfs = sampleGvcf :: gvcfPool
- gatkGenotyping.samples :+= sampleName
- gatkGenotyping.outputDir = new File(outputDir, "samples_" + gvcfPool.size)
- gatkGenotyping.init()
- gatkGenotyping.biopetScript()
- addAll(gatkGenotyping.functions)
- }
-}
-
-object GatkBenchmarkGenotyping extends PipelineCommand
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
deleted file mode 100644
index 2f54cbbc70bc7c2666ef9c043017603c0b1c4b9f..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ /dev/null
@@ -1,61 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
-import org.broadinstitute.gatk.queue.QScript
-
-class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "Gvcf files", shortName = "I")
- var inputGvcfs: List[File] = Nil
-
- @Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference")
-
- @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = config("dbsnp")
-
- @Argument(doc = "OutputName", required = false)
- var outputName: String = "genotype"
-
- @Output(doc = "OutputFile", shortName = "O", required = false)
- var outputFile: File = _
-
- @Argument(doc = "Samples", shortName = "sample", required = false)
- var samples: List[String] = Nil
-
- def init() {
- require(outputName != null, "Outputname is null")
- if (outputFile == null) outputFile = new File(outputDir, outputName + ".vcf.gz")
- }
-
- def biopetScript() {
- addGenotypeGVCFs(inputGvcfs, outputFile)
- if (samples.nonEmpty) {
- if (samples.size > 1) addSelectVariants(outputFile, samples, new File(outputDir, "samples/"), "all")
- for (sample <- samples) addSelectVariants(outputFile, List(sample), new File(outputDir, "samples/"), sample)
- }
- }
-
- def addGenotypeGVCFs(gvcfFiles: List[File], outputFile: File): File = {
- val genotypeGVCFs = GenotypeGVCFs(this, gvcfFiles, outputFile)
- add(genotypeGVCFs)
- genotypeGVCFs.out
- }
-
- def addSelectVariants(inputFile: File, samples: List[String], outputDir: File, name: String) {
- val selectVariants = SelectVariants(this, inputFile, new File(outputDir, name + ".vcf.gz"))
- selectVariants.excludeNonVariants = true
- for (sample <- samples) selectVariants.sample_name :+= sample
- add(selectVariants)
- }
-}
-
-object GatkGenotyping extends PipelineCommand
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
deleted file mode 100644
index 3707ec2751cd21c82193f65c47281d294a764778..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ /dev/null
@@ -1,235 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
-import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
-import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
-import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import org.broadinstitute.gatk.queue.QScript
-
-import scala.collection.JavaConversions._
-
-class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
- qscript =>
- def this() = this(null)
-
- @Argument(doc = "Skip Genotyping step", shortName = "skipgenotyping", required = false)
- var skipGenotyping: Boolean = config("skip_genotyping", default = false)
-
- /** Merge gvcfs */
- var mergeGvcfs: Boolean = config("merge_gvcfs", default = false)
-
- /** Joint variantcalling */
- var jointVariantcalling: Boolean = config("joint_variantcalling", default = false)
-
- /** Joint genotyping */
- var jointGenotyping: Boolean = config("joint_genotyping", default = false)
-
- var singleSampleCalling = config("single_sample_calling", default = true)
- var reference: File = config("reference")
- var useAllelesOption: Boolean = config("use_alleles_option", default = false)
- val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
-
- def summaryFile = new File(outputDir, "GatkPipeline.summary.json")
-
- //TODO: Add summary
- def summaryFiles = Map()
-
- //TODO: Add summary
- def summarySettings = Map()
-
- def makeSample(id: String) = new Sample(id)
- class Sample(sampleId: String) extends AbstractSample(sampleId) {
- //TODO: Add summary
- def summaryFiles: Map[String, File] = Map()
-
- //TODO: Add summary
- def summaryStats: Map[String, Any] = Map()
-
- def makeLibrary(id: String) = new Library(id)
- class Library(libId: String) extends AbstractLibrary(libId) {
- //TODO: Add summary
- def summaryFiles: Map[String, File] = Map()
-
- //TODO: Add summary
- def summaryStats: Map[String, Any] = Map()
-
- val mapping = new Mapping(qscript)
- mapping.sampleId = Some(sampleId)
- mapping.libId = Some(libId)
- mapping.outputDir = libDir
-
- /** Library variantcalling */
- val gatkVariantcalling = new GatkVariantcalling(qscript)
- gatkVariantcalling.doublePreProces = false
- gatkVariantcalling.sampleID = sampleId
- gatkVariantcalling.outputDir = new File(libDir, "variantcalling")
-
- protected def addJobs(): Unit = {
- val bamFile: Option[File] = if (config.contains("R1")) {
- mapping.input_R1 = config("R1")
- mapping.input_R2 = config("R2")
- mapping.init()
- mapping.biopetScript()
- addAll(mapping.functions) // Add functions of mapping to curent function pool
- Some(mapping.finalBamFile)
- } else if (config.contains("bam")) {
- var bamFile: File = config("bam")
- if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
-
- if (config("bam_to_fastq", default = false).asBoolean) {
- val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libId + ".R1.fastq",
- libDir + sampleId + "-" + libId + ".R2.fastq")
- samToFastq.isIntermediate = true
- qscript.add(samToFastq)
- mapping.input_R1 = samToFastq.fastqR1
- mapping.input_R2 = Some(samToFastq.fastqR2)
- mapping.init()
- mapping.biopetScript()
- addAll(mapping.functions) // Add functions of mapping to curent function pool
- Some(mapping.finalBamFile)
- } else {
- var readGroupOke = true
- val inputSam = SamReaderFactory.makeDefault.open(bamFile)
- val header = inputSam.getFileHeader.getReadGroups
- for (readGroup <- inputSam.getFileHeader.getReadGroups) {
- if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
- if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
- if (readGroup.getSample != sampleId || readGroup.getLibrary != libId) readGroupOke = false
- }
- inputSam.close()
-
- if (!readGroupOke) {
- if (config("correct_readgroups", default = false)) {
- logger.info("Correcting readgroups, file:" + bamFile)
- val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libId + ".bam"))
- aorrg.RGID = sampleId + "-" + libId
- aorrg.RGLB = libId
- aorrg.RGSM = sampleId
- aorrg.isIntermediate = true
- qscript.add(aorrg)
- bamFile = aorrg.output
- } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
- "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
- }
- addAll(BamMetrics(qscript, bamFile, libDir + "metrics/").functions)
-
- Some(bamFile)
- }
- } else {
- logger.error("Sample: " + sampleId + ": No R1 found for run: " + libId)
- None
- }
-
- if (bamFile.isDefined) {
- gatkVariantcalling.inputBams = List(bamFile.get)
- gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
- gatkVariantcalling.init()
- gatkVariantcalling.biopetScript()
- addAll(gatkVariantcalling.functions)
- }
-
- addSummaryQScript(mapping)
- }
- }
-
- /** sample variantcalling */
- val gatkVariantcalling = new GatkVariantcalling(qscript)
- gatkVariantcalling.sampleID = sampleId
- gatkVariantcalling.outputDir = new File(sampleDir, "variantcalling")
-
- protected def addJobs(): Unit = {
- addPerLibJobs()
- gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
- gatkVariantcalling.preProcesBams = false
- if (!singleSampleCalling) {
- gatkVariantcalling.useHaplotypecaller = false
- gatkVariantcalling.useUnifiedGenotyper = false
- }
- gatkVariantcalling.init()
- gatkVariantcalling.biopetScript()
- addAll(gatkVariantcalling.functions)
-
- gatkVariantcalling.inputBams.foreach(x => addAll(Bam2Wig(qscript, x).functions))
- }
- }
-
- def init() {
- }
-
- val multisampleVariantcalling = new GatkVariantcalling(this) {
- override def configName = "gatkvariantcalling"
- override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
- }
-
- def biopetScript(): Unit = {
- addSamplesJobs()
-
- addSummaryJobs()
- }
-
- def addMultiSampleJobs(): Unit = {
- val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {
- val newFile = new File(outputDir, "merged.gvcf.vcf.gz")
- add(CombineGVCFs(this, externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile), newFile))
- List(newFile)
- } else externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile)
-
- if (!skipGenotyping && gvcfFiles.nonEmpty) {
- if (jointGenotyping) {
- val gatkGenotyping = new GatkGenotyping(this)
- gatkGenotyping.inputGvcfs = gvcfFiles
- gatkGenotyping.outputDir = new File(outputDir, "genotyping")
- gatkGenotyping.init()
- gatkGenotyping.biopetScript()
- addAll(gatkGenotyping.functions)
- var vcfFile = gatkGenotyping.outputFile
- }
- } else logger.warn("No gVCFs to genotype")
-
- if (jointVariantcalling) {
- val allBamfiles = samples.map(_._2.gatkVariantcalling.scriptOutput.bamFiles).toList.fold(Nil)(_ ++ _)
- val allRawVcfFiles = samples.map(_._2.gatkVariantcalling.scriptOutput.rawVcfFile).filter(_ != null).toList
-
- val gatkVariantcalling = new GatkVariantcalling(this) {
- override def configName = "gatkvariantcalling"
- override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
- }
-
- if (gatkVariantcalling.useMpileup) {
- val cvRaw = CombineVariants(this, allRawVcfFiles.toList, new File(outputDir, "variantcalling/multisample.raw.vcf.gz"))
- add(cvRaw)
- gatkVariantcalling.rawVcfInput = cvRaw.out
- }
-
- multisampleVariantcalling.preProcesBams = false
- multisampleVariantcalling.doublePreProces = false
- multisampleVariantcalling.inputBams = allBamfiles.toList
- multisampleVariantcalling.outputDir = new File(outputDir, "variantcalling")
- multisampleVariantcalling.outputName = "multisample"
- multisampleVariantcalling.init()
- multisampleVariantcalling.biopetScript()
- addAll(multisampleVariantcalling.functions)
-
- if (config("inputtype", default = "dna").asString != "rna" && config("recalibration", default = false).asBoolean) {
- val recalibration = new GatkVariantRecalibration(this)
- recalibration.inputVcf = multisampleVariantcalling.scriptOutput.finalVcfFile
- recalibration.bamFiles = allBamfiles
- recalibration.outputDir = new File(outputDir, "recalibration")
- recalibration.init()
- recalibration.biopetScript()
- }
- }
- }
-}
-
-object GatkPipeline extends PipelineCommand
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
deleted file mode 100644
index 772aa6887d7a7e4983059f84ea3ac7b455880c4a..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+++ /dev/null
@@ -1,76 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
-import org.broadinstitute.gatk.queue.QScript
-
-class GatkVariantRecalibration(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "input vcf file", shortName = "I")
- var inputVcf: File = _
-
- @Input(doc = "input vcf file", shortName = "BAM", required = false)
- var bamFiles: List[File] = Nil
-
- @Output(doc = "output vcf file", shortName = "out")
- var outputVcf: File = _
-
- def init() {
- require(inputVcf != null, "Missing Output directory on gatk module")
- }
-
- def biopetScript() {
- var vcfFile: File = if (bamFiles.nonEmpty) addVariantAnnotator(inputVcf, bamFiles, outputDir) else inputVcf
- vcfFile = addSnpVariantRecalibrator(vcfFile, outputDir)
- vcfFile = addIndelVariantRecalibrator(vcfFile, outputDir)
- }
-
- def addSnpVariantRecalibrator(inputVcf: File, dir: File): File = {
- val snpRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
- swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = false)
- if (snpRecal.resource.nonEmpty) {
- add(snpRecal)
-
- val snpApply = ApplyRecalibration(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal.vcf"),
- snpRecal.recal_file, snpRecal.tranches_file, indel = false)
- add(snpApply)
-
- snpApply.out
- } else {
- logger.warn("Skipped snp Recalibration, resource is missing")
- inputVcf
- }
- }
-
- def addIndelVariantRecalibrator(inputVcf: File, dir: File): File = {
- val indelRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
- swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = true)
- if (indelRecal.resource.nonEmpty) {
- add(indelRecal)
-
- val indelApply = ApplyRecalibration(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal.vcf"),
- indelRecal.recal_file, indelRecal.tranches_file, indel = true)
- add(indelApply)
-
- indelApply.out
- } else {
- logger.warn("Skipped indel Recalibration, resource is missing")
- inputVcf
- }
- }
-
- def addVariantAnnotator(inputvcf: File, bamfiles: List[File], dir: File): File = {
- val variantAnnotator = VariantAnnotator(this, inputvcf, bamfiles, swapExt(dir, inputvcf, ".vcf", ".anotated.vcf"))
- add(variantAnnotator)
- variantAnnotator.out
- }
-}
-
-object GatkVariantRecalibration extends PipelineCommand
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
deleted file mode 100644
index 750cbee21adea6c059d939aad518ca9aed0eb06e..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ /dev/null
@@ -1,272 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.extensions.Ln
-import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
-import nl.lumc.sasc.biopet.extensions.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-
-import scala.collection.SortedMap
-import scala.language.reflectiveCalls
-
-class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- val scriptOutput = new GatkVariantcalling.ScriptOutput
-
- @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM")
- var inputBams: List[File] = Nil
-
- @Input(doc = "Raw vcf file", shortName = "raw")
- var rawVcfInput: File = _
-
- @Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference")
-
- @Argument(doc = "OutputName", required = false)
- var outputName: String = _
-
- @Argument(doc = "Sample name", required = false)
- var sampleID: String = _
-
- var preProcesBams: Boolean = config("pre_proces_bams", default = true)
- var variantcalling: Boolean = true
- var doublePreProces: Boolean = config("double_pre_proces", default = true)
- var useHaplotypecaller: Boolean = config("use_haplotypecaller", default = true)
- var useUnifiedGenotyper: Boolean = config("use_unifiedgenotyper", default = false)
- var useAllelesOption: Boolean = config("use_alleles_option", default = false)
- var useMpileup: Boolean = config("use_mpileup", default = true)
- var useIndelRealigner: Boolean = config("use_indel_realign", default = true)
- var useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
-
- def init() {
- if (outputName == null && sampleID != null) outputName = sampleID
- else if (outputName == null) outputName = config("output_name", default = "noname")
-
- val baseRecalibrator = new BaseRecalibrator(this)
- if (preProcesBams && useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
- logger.warn("No Known site found, skipping base recalibration")
- useBaseRecalibration = false
- }
- }
-
- private def doublePreProces(files: List[File]): List[File] = {
- if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
- else if (!doublePreProces) files
- else if (files.size == 1) {
- val bamFile = new File(outputDir, files.head.getName)
- if (bamFile != files.head) {
- val oldIndex: File = new File(files.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex: File = swapExt(outputDir, bamFile, ".bam", ".bai")
- val baiLn = Ln(this, oldIndex, newIndex)
- add(baiLn)
-
- val bamLn = Ln(this, files.head, bamFile)
- bamLn.deps :+= baiLn.output
- add(bamLn)
- }
- List(bamFile)
- } else {
- val markDup = MarkDuplicates(this, files, new File(outputDir, outputName + ".dedup.bam"))
- markDup.isIntermediate = useIndelRealigner
- add(markDup)
- if (useIndelRealigner) {
- List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
- } else {
- List(markDup.output)
- }
- }
- }
-
- def biopetScript() {
- scriptOutput.bamFiles = {
- doublePreProces(if (preProcesBams) {
- for (inputBam <- inputBams) yield {
- var bamFile = inputBam
- if (useIndelRealigner)
- bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
- if (useBaseRecalibration)
- bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = inputBams.size > 1)
- bamFile
- }
- } else {
- inputBams
- })
- }
-
- if (variantcalling) {
- var mergBuffer: SortedMap[String, File] = SortedMap()
- def mergeList = mergBuffer map { case (key, file) => TaggedFile(removeNoneVariants(file), "name=" + key) }
-
- if (sampleID != null && (useHaplotypecaller || config("joint_genotyping", default = false).asBoolean)) {
- val hcGvcf = new HaplotypeCaller(this)
- hcGvcf.useGvcf()
- hcGvcf.input_file = scriptOutput.bamFiles
- hcGvcf.out = new File(outputDir, outputName + ".hc.discovery.gvcf.vcf.gz")
- add(hcGvcf)
- scriptOutput.gvcfFile = hcGvcf.out
- }
-
- if (useHaplotypecaller) {
- if (sampleID != null) {
- val genotypeGVCFs = GenotypeGVCFs(this, List(scriptOutput.gvcfFile), new File(outputDir, outputName + ".hc.discovery.vcf.gz"))
- add(genotypeGVCFs)
- scriptOutput.hcVcfFile = genotypeGVCFs.out
- } else {
- val hcGvcf = new HaplotypeCaller(this)
- hcGvcf.input_file = scriptOutput.bamFiles
- hcGvcf.out = new File(outputDir, outputName + ".hc.discovery.vcf.gz")
- add(hcGvcf)
- scriptOutput.hcVcfFile = hcGvcf.out
- }
- mergBuffer += ("1.HC-Discovery" -> scriptOutput.hcVcfFile)
- }
-
- if (useUnifiedGenotyper) {
- val ugVcf = new UnifiedGenotyper(this)
- ugVcf.input_file = scriptOutput.bamFiles
- ugVcf.out = new File(outputDir, outputName + ".ug.discovery.vcf.gz")
- add(ugVcf)
- scriptOutput.ugVcfFile = ugVcf.out
- mergBuffer += ("2.UG-Discovery" -> scriptOutput.ugVcfFile)
- }
-
- // Generate raw vcf
- if (useMpileup) {
- if (sampleID != null && scriptOutput.bamFiles.size == 1) {
- val m2v = new MpileupToVcf(this)
- m2v.inputBam = scriptOutput.bamFiles.head
- m2v.sample = sampleID
- m2v.output = new File(outputDir, outputName + ".raw.vcf")
- add(m2v)
- scriptOutput.rawVcfFile = m2v.output
-
- val vcfFilter = new VcfFilter(this) {
- override def defaults = Map("min_sample_depth" -> 8,
- "min_alternate_depth" -> 2,
- "min_samples_pass" -> 1,
- "filter_ref_calls" -> true
- )
- }
- vcfFilter.inputVcf = m2v.output
- vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
- add(vcfFilter)
- scriptOutput.rawFilterVcfFile = vcfFilter.outputVcf
- } else if (rawVcfInput != null) scriptOutput.rawFilterVcfFile = rawVcfInput
- if (scriptOutput.rawFilterVcfFile != null) mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
- }
-
- // Allele mode
- if (useAllelesOption) {
- val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
- mergeAlleles.isIntermediate = true
- add(mergeAlleles)
-
- if (useHaplotypecaller) {
- val hcAlleles = new HaplotypeCaller(this)
- hcAlleles.input_file = scriptOutput.bamFiles
- hcAlleles.out = new File(outputDir, outputName + ".hc.allele.vcf.gz")
- hcAlleles.alleles = mergeAlleles.output
- hcAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
- add(hcAlleles)
- scriptOutput.hcAlleleVcf = hcAlleles.out
- mergBuffer += ("3.HC-alleles" -> hcAlleles.out)
- }
-
- if (useUnifiedGenotyper) {
- val ugAlleles = new UnifiedGenotyper(this)
- ugAlleles.input_file = scriptOutput.bamFiles
- ugAlleles.out = new File(outputDir, outputName + ".ug.allele.vcf.gz")
- ugAlleles.alleles = mergeAlleles.output
- ugAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
- add(ugAlleles)
- scriptOutput.ugAlleleVcf = ugAlleles.out
- mergBuffer += ("4.UG-alleles" -> ugAlleles.out)
- }
- }
-
- def removeNoneVariants(input: File): File = {
- val output = input.getAbsolutePath.stripSuffix(".vcf.gz") + ".variants_only.vcf.gz"
- val sv = SelectVariants(this, input, output)
- sv.excludeFiltered = true
- sv.excludeNonVariants = true
- sv.isIntermediate = true
- add(sv)
- sv.out
- }
-
- val cvFinal = CombineVariants(this, mergeList.toList, new File(outputDir, outputName + ".final.vcf.gz"))
- cvFinal.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
- add(cvFinal)
-
- val vcfStats = new VcfStats(this)
- vcfStats.input = cvFinal.out
- vcfStats.setOutputDir(new File(outputDir, "vcfstats"))
- add(vcfStats)
-
- scriptOutput.finalVcfFile = cvFinal.out
- }
- }
-
- def addIndelRealign(inputBam: File, dir: File, isIntermediate: Boolean = true): File = {
- val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
- realignerTargetCreator.isIntermediate = true
- add(realignerTargetCreator)
-
- val indelRealigner = IndelRealigner(this, inputBam, realignerTargetCreator.out, dir)
- indelRealigner.isIntermediate = isIntermediate
- add(indelRealigner)
-
- indelRealigner.o
- }
-
- def addBaseRecalibrator(inputBam: File, dir: File, isIntermediate: Boolean = false): File = {
- val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
-
- if (baseRecalibrator.knownSites.isEmpty) {
- logger.warn("No Known site found, skipping base recalibration, file: " + inputBam)
- return inputBam
- }
- add(baseRecalibrator)
-
- if (config("use_analyze_covariates", default = false).asBoolean) {
- val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
- baseRecalibratorAfter.BQSR = baseRecalibrator.o
- add(baseRecalibratorAfter)
-
- add(AnalyzeCovariates(this, baseRecalibrator.o, baseRecalibratorAfter.o, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
- }
-
- val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
- printReads.BQSR = baseRecalibrator.o
- printReads.isIntermediate = isIntermediate
- add(printReads)
-
- printReads.o
- }
-}
-
-object GatkVariantcalling extends PipelineCommand {
- class ScriptOutput {
- var bamFiles: List[File] = _
- var gvcfFile: File = _
- var hcVcfFile: File = _
- var ugVcfFile: File = _
- var rawVcfFile: File = _
- var rawFilterVcfFile: File = _
- var hcAlleleVcf: File = _
- var ugAlleleVcf: File = _
- var finalVcfFile: File = _
- }
-}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index eae23a65406c85035ae38a939c11f4ac3d25af66..620619bfea1ccdb745f814d2b801c100437d4c76 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaTrait }
import org.broadinstitute.gatk.queue.QScript
/**
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
index 1878d86fd150af451ab46fb69234ccbb66b05ec2..edbc633f3a03204f3d4e50ac14bc016134825252 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
@@ -6,9 +6,9 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.broad.GenotypeGVCFs
+import nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
@@ -22,99 +22,13 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
/** Will generate all available variantcallers */
override def callersList = {
- new HaplotypeCallerGvcf ::
- new HaplotypeCallerAllele ::
- new UnifiedGenotyperAllele ::
- new UnifiedGenotyper ::
- new HaplotypeCaller ::
+ new HaplotypeCallerGvcf(this) ::
+ new HaplotypeCallerAllele(this) ::
+ new UnifiedGenotyperAllele(this) ::
+ new UnifiedGenotyper(this) ::
+ new HaplotypeCaller(this) ::
super.callersList
}
-
- /** Default mode for the haplotypecaller */
- class HaplotypeCaller extends Variantcaller {
- val name = "haplotypecaller"
- protected val defaultPrio = 1
-
- def outputFile = new File(outputDir, namePrefix + ".haplotypecaller.vcf.gz")
-
- def addJobs() {
- val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
- hc.input_file = inputBams
- hc.out = outputFile
- add(hc)
- }
- }
-
- /** Default mode for UnifiedGenotyper */
- class UnifiedGenotyper extends Variantcaller {
- val name = "unifiedgenotyper"
- protected val defaultPrio = 20
-
- def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper.vcf.gz")
-
- def addJobs() {
- val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
- ug.input_file = inputBams
- ug.out = outputFile
- add(ug)
- }
- }
-
- /** Allele mode for Haplotypecaller */
- class HaplotypeCallerAllele extends Variantcaller {
- val name = "haplotypecaller_allele"
- protected val defaultPrio = 5
-
- def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_allele.vcf.gz")
-
- def addJobs() {
- val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
- hc.input_file = inputBams
- hc.out = outputFile
- hc.alleles = config("input_alleles")
- hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
- add(hc)
- }
- }
-
- /** Allele mode for GenotyperAllele */
- class UnifiedGenotyperAllele extends Variantcaller {
- val name = "unifiedgenotyper_allele"
- protected val defaultPrio = 9
-
- def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper_allele.vcf.gz")
-
- def addJobs() {
- val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
- ug.input_file = inputBams
- ug.out = outputFile
- ug.alleles = config("input_alleles")
- ug.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
- add(ug)
- }
- }
-
- /** Gvcf mode for haplotypecaller */
- class HaplotypeCallerGvcf extends Variantcaller {
- val name = "haplotypecaller_gvcf"
- protected val defaultPrio = 5
-
- def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_gvcf.vcf.gz")
-
- def addJobs() {
- val gvcfFiles = for (inputBam <- inputBams) yield {
- val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
- hc.input_file = List(inputBam)
- hc.out = new File(outputDir, inputBam.getName.stripSuffix(".bam") + ".gvcf.vcf.gz")
- hc.useGvcf()
- add(hc)
- hc.out
- }
-
- val genotypeGVCFs = GenotypeGVCFs(qscript, gvcfFiles, outputFile)
- add(genotypeGVCFs)
- }
- }
}
/** object to add default main method to pipeline */
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f18b16812b48375bb7e1d57969ef9b1db7ba5691
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala
@@ -0,0 +1,17 @@
+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.broad
+
+/** Default mode for the haplotypecaller */
+class HaplotypeCaller(val root: Configurable) extends Variantcaller {
+ val name = "haplotypecaller"
+ protected def defaultPrio = 1
+
+ def biopetScript() {
+ val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
+ add(hc)
+ }
+}
+
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala
new file mode 100644
index 0000000000000000000000000000000000000000..a4bff551c7bff4a6376d16d8b0401b008a6aad8e
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala
@@ -0,0 +1,18 @@
+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.broad
+
+/** Allele mode for Haplotypecaller */
+class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
+ val name = "haplotypecaller_allele"
+ protected def defaultPrio = 5
+
+ def biopetScript() {
+ val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
+ hc.alleles = config("input_alleles")
+ hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+ add(hc)
+ }
+}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala
new file mode 100644
index 0000000000000000000000000000000000000000..cf289cb789e4c5ad944b30eb0b71b163cc1115ff
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala
@@ -0,0 +1,22 @@
+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.broad
+
+/** Gvcf mode for haplotypecaller */
+class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
+ val name = "haplotypecaller_gvcf"
+ protected def defaultPrio = 5
+
+ def biopetScript() {
+ val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
+ val hc = broad.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
+ add(hc)
+ hc.out
+ }
+
+ val genotypeGVCFs = broad.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+ add(genotypeGVCFs)
+ }
+}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b71273b284c153ed628565d23c8ca0dffd7bd010
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala
@@ -0,0 +1,16 @@
+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.broad
+
+/** Default mode for UnifiedGenotyper */
+class UnifiedGenotyper(val root: Configurable) extends Variantcaller {
+ val name = "unifiedgenotyper"
+ protected def defaultPrio = 20
+
+ def biopetScript() {
+ val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
+ add(ug)
+ }
+}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
new file mode 100644
index 0000000000000000000000000000000000000000..61bb63ae3f897cc29bd37fc4c8af53f874faad28
--- /dev/null
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
@@ -0,0 +1,18 @@
+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.broad
+
+/** Allele mode for GenotyperAllele */
+class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
+ val name = "unifiedgenotyper_allele"
+ protected def defaultPrio = 9
+
+ def biopetScript() {
+ val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
+ ug.alleles = config("input_alleles")
+ ug.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+ add(ug)
+ }
+}
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 bd78727cad7e431d9af8dceaa8a4f6aef4c1d163..14207e5a829de7fd7cae4738a10fd9f6b28c5546 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
@@ -76,7 +76,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
+ pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
val illegalArgumentException = pipeline.inputBams.isEmpty ||
(!raw && !bcftools &&
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
index f1bae9632f6bb046360496b0bf924515b791f794..af29b48fab64495b517427e08b416f161f7443cd 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
@@ -10,7 +10,7 @@
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
-<%@ var target: String %>
+<%@ var target: Option[String] %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
@@ -46,7 +46,7 @@
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
- val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
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]
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
index 8aea9602a65fd2282e38909b170722151ac13603..a89c4eb4cb5262adce57afe546f89db2e49b6849 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
@@ -8,13 +8,13 @@
<%@ var libId: Option[String] = None %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
-<%@ var target: String %>
+<%@ var target: Option[String] %>
#{
- val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
+ val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target.get + "_cov_stats", "plot", "path")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
- val plot = new File(outputDir, target + "_cov_stats.png")
+ val plot = new File(outputDir, target.get + "_cov_stats.png")
- val values = summary.getValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+ val values = summary.getValue(sampleId, libId, metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index f0c9478603de90f9401241bfcebf797d24196f52..61f4243261df710a4ef7c19780a7bcc13146e790 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -30,19 +30,14 @@ import org.broadinstitute.gatk.queue.QScript
class BamMetrics(val root: Configurable) extends QScript
with SummaryQScript
with SampleLibraryTag
- with Reference {
+ with Reference
+ with TargetRegions {
def this() = this(null)
@Input(doc = "Bam File", shortName = "BAM", required = true)
var inputBam: File = _
- /** Bed files for region of interests */
- var roiBedFiles: List[File] = config("regions_of_interest", Nil)
-
- /** Bed of amplicon that is used */
- var ampliconBedFile: Option[File] = config("amplicon_bed")
-
/** Settings for CollectRnaSeqMetrics */
var rnaMetricsSettings: Map[String, String] = Map()
var transcriptRefFlatFile: Option[File] = config("transcript_refflat")
@@ -145,7 +140,7 @@ class BamMetrics(val root: Configurable) extends QScript
val pcrMetrics = CollectTargetedPcrMetrics(this, inputBam,
ampIntervals, ampIntervals :: roiIntervals.map(_.intervals), outputDir)
add(pcrMetrics)
- addSummarizable(chsMetrics, "targeted_pcr_metrics")
+ addSummarizable(pcrMetrics, "targeted_pcr_metrics")
Intervals(bedFile, ampIntervals)
}
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index 78377793adc53b335e60300afece9f2a49cf3fd6..4da9ec9e5f878262e66473d559cc209580674992 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -70,7 +70,7 @@ object BammetricsReport extends ReportBuilder {
if (targets.isEmpty) List()
else List("Targets" -> ReportPage(
List(),
- targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> t))),
+ targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
Map())),
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
new file mode 100644
index 0000000000000000000000000000000000000000..01c6568c848479dc429b68c771b7f987cc4c9bd6
--- /dev/null
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
@@ -0,0 +1,16 @@
+package nl.lumc.sasc.biopet.pipelines.bammetrics
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by pjvan_thof on 11/20/15.
+ */
+trait TargetRegions extends Configurable {
+ /** Bed files for region of interests */
+ var roiBedFiles: List[File] = config("regions_of_interest", Nil)
+
+ /** Bed of amplicon that is used */
+ var ampliconBedFile: Option[File] = config("amplicon_bed")
+}
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index 7da7f9c3ce26248867468bb59398533a87cd007e..675d4d7557be2edf84c41494edfaa30af9d13a78 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
@@ -27,9 +27,10 @@ import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.QScript
trait BastyTrait extends MultiSampleQScript {
- qscript =>
+ qscript: QScript =>
case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
diff --git a/public/biopet-core/pom.xml b/public/biopet-core/pom.xml
index 378295317cb5b79835f6023b4b56a3a455a4d8fe..c2064007a268ffa2a822eb4565a95acb52448a40 100644
--- a/public/biopet-core/pom.xml
+++ b/public/biopet-core/pom.xml
@@ -57,7 +57,7 @@
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
- <version>3.4</version>
+ <version>3.5</version>
<exclusions>
<exclusion>
<groupId>org.broadinstitute.gatk</groupId>
@@ -68,7 +68,7 @@
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-extensions-public</artifactId>
- <version>3.4</version>
+ <version>3.5</version>
</dependency>
<dependency>
<groupId>org.scalatra.scalate</groupId>
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 66c54134218b47a1978fb21efe5393ea782b91a5..c95299b0d4c47ef189a22fce2fcd1dfaff9183f8 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -17,17 +17,18 @@ package nl.lumc.sasc.biopet.core
import java.io.File
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.utils.commandline.Argument
/** Base for biopet pipeline */
-trait BiopetQScript extends Configurable with GatkLogging {
+trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
@Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
@@ -125,6 +126,24 @@ trait BiopetQScript extends Configurable with GatkLogging {
function.isIntermediate = isIntermediate
add(function)
}
+
+ def add(subPipeline: QScript): Unit = {
+ subPipeline.qSettings = this.qSettings
+ subPipeline match {
+ case that: SummaryQScript =>
+ that.init()
+ that.biopetScript()
+ this match {
+ case s: SummaryQScript => s.addSummaryQScript(that)
+ case _ =>
+ }
+ case that: BiopetQScript =>
+ that.init()
+ that.biopetScript()
+ case _ => subPipeline.script
+ }
+ addAll(subPipeline.functions)
+ }
}
object BiopetQScript {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 81c992b4d5911af0b9a808e7750d15f1078c44e9..fa4f40645b49efee9ba5fb9c42a05c1c10006b0d 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -19,11 +19,11 @@ import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
+import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.Argument
/** This trait creates a structured way of use multisample pipelines */
-trait MultiSampleQScript extends SummaryQScript {
- qscript =>
+trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
@Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
private[core] val onlySamples: List[String] = Nil
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index bcdabfaeb1f95ed3bade6df058b3b9ae2b291f96..152230c8a41c18e28b69e3c5fb9d10febe8eec68 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -132,7 +132,10 @@ object Reference {
* @param fastaFile Fasta file
*/
def requireDict(fastaFile: File): Unit = {
- val dict = new File(fastaFile.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+ val dict = new File(fastaFile.getAbsolutePath
+ .stripSuffix(".fna")
+ .stripSuffix(".fa")
+ .stripSuffix(".fasta") + ".dict")
if (!dict.exists()) Logging.addError("Reference is missing a dict file")
}
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index a1568a9b82f0f16ee691d755b0841c4038fcb7b0..0e947ba6c7d3bbf144c98feb1b7cb21601c6629f 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
+import org.broadinstitute.gatk.queue.QScript
import scala.collection.mutable
@@ -27,7 +28,7 @@ import scala.collection.mutable
*
* Created by pjvan_thof on 2/14/15.
*/
-trait SummaryQScript extends BiopetQScript { qscript =>
+trait SummaryQScript extends BiopetQScript { qscript: QScript =>
/** Key is sample/library, None is sample or library is not applicable */
private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
@@ -91,8 +92,11 @@ trait SummaryQScript extends BiopetQScript { qscript =>
summaryQScripts :+= summaryQScript
}
+ private var addedJobs = false
+
/** Add jobs to qscript to execute summary, also add checksum jobs */
def addSummaryJobs(): Unit = {
+ if (addedJobs) throw new IllegalStateException("Summary jobs for this QScript are already executed")
val writeSummary = new WriteSummary(this)
def addChecksum(file: File): Unit = {
@@ -159,6 +163,8 @@ trait SummaryQScript extends BiopetQScript { qscript =>
logger.info("Write summary is skipped because sample flag is used")
case _ => add(writeSummary)
}
+
+ addedJobs = true
}
}
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
index 295164106beebe99b2eee2398bbd79c6aff2b7ce..fb8c5a422359040ba6bf53ec78c78020853a470e 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala
@@ -20,6 +20,8 @@ import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
+import scala.language.reflectiveCalls
+
/**
* Created by pjvanthof on 17/11/15.
*/
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index e8f9c2caf43ff1163218a5814bfa0ba45f0b6ceb..6e06894f916a5206bcac748d924eb8f3a9f51c53 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -43,6 +43,9 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
def versionCommand = executable + " --version"
def versionRegex = """(.*)""".r
+ /** Name of the key containing clipped adapters information in the summary stats. */
+ def adaptersStatsName = "adapters"
+
var default_clip_mode: String = config("default_clip_mode", default = "3")
var opt_adapter: Set[String] = config("adapter", default = Nil)
var opt_anywhere: Set[String] = config("anywhere", default = Nil)
@@ -89,7 +92,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
Map("num_reads_affected" -> stats("trimmed"),
"num_reads_discarded_too_short" -> stats("tooshort"),
"num_reads_discarded_too_long" -> stats("toolong"),
- "adapters" -> adapter_stats.toMap
+ adaptersStatsName -> adapter_stats.toMap
)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
index daaaf73d96c7d190c61bbdbc45331115eb388aed..a94561d8bc0c2aec368148b20e159e08e2e56ef0 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -56,7 +56,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction with Versi
var l: Boolean = config("l", default = false)
var f: Boolean = config("f", default = false)
- executable = config("exe", default = "tabix")
+ executable = config("exe", default = "tabix", freeVar = false)
def versionCommand = executable
def versionRegex = """Version: (.*)""".r
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
index 6e7bf4146464e9c6f69e7759569985fce7204e23..2291df063b26293132bbd95c9f8ccf56c8ddfd13 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
abstract class Bcftools extends BiopetCommandLineFunction with Version {
override def subPath = "bcftools" :: super.subPath
- executable = config("exe", default = "bcftools")
+ executable = config("exe", default = "bcftools", submodule = "bcftools", freeVar = false)
def versionCommand = executable
def versionRegex = """Version: (.*)""".r
override def versionExitcode = List(0, 1)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
deleted file mode 100644
index 9f662e3d7830f542a7361c11c5803385afef44ac..0000000000000000000000000000000000000000
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
+++ /dev/null
@@ -1,80 +0,0 @@
-/**
- * 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.breakdancer
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
-class Breakdancer(val root: Configurable) extends QScript with BiopetQScript with Reference {
- def this() = this(null)
-
- @Input(doc = "Input file (bam)")
- var input: File = _
-
- @Argument(doc = "Work directory")
- var workDir: File = _
-
- var deps: List[File] = Nil
-
- @Output(doc = "Breakdancer config")
- lazy val configfile: File = {
- new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.cfg")
- }
- @Output(doc = "Breakdancer raw output")
- lazy val outputraw: File = {
- new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.tsv")
- }
- @Output(doc = "Breakdancer VCF output")
- lazy val outputvcf: File = {
- new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.vcf")
- }
-
- override def init(): Unit = {
- }
-
- def biopetScript() {
- // read config and set all parameters for the pipeline
- logger.info("Starting Breakdancer configuration")
-
- val bdcfg = BreakdancerConfig(this, input, this.configfile)
- bdcfg.deps = this.deps
- outputFiles += ("cfg" -> bdcfg.output)
- add(bdcfg)
-
- val breakdancer = BreakdancerCaller(this, bdcfg.output, this.outputraw)
- add(breakdancer)
- outputFiles += ("tsv" -> breakdancer.output)
-
- val bdvcf = BreakdancerVCF(this, breakdancer.output, this.outputvcf)
- add(bdvcf)
- outputFiles += ("vcf" -> bdvcf.output)
- }
-}
-
-object Breakdancer extends PipelineCommand {
- def apply(root: Configurable, input: File, runDir: File): Breakdancer = {
- val breakdancer = new Breakdancer(root)
- breakdancer.input = input
- breakdancer.workDir = runDir
- breakdancer.init()
- breakdancer.biopetScript()
- breakdancer
- }
-}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
deleted file mode 100644
index b5fabe35e56555ba1723ab9270c04578b6bde23e..0000000000000000000000000000000000000000
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
+++ /dev/null
@@ -1,124 +0,0 @@
-/**
- * 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.delly
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
-
-class Delly(val root: Configurable) extends QScript with BiopetQScript with Reference {
- def this() = this(null)
-
- @Input(doc = "Input file (bam)")
- var input: File = _
-
- var workDir: File = _
-
- @Output(doc = "Delly result VCF")
- var outputVcf: File = _
-
- var outputName: String = _
-
- // select the analysis types DEL,DUP,INV,TRA
- var del: Boolean = config("DEL", default = true)
- var dup: Boolean = config("DUP", default = true)
- var inv: Boolean = config("INV", default = true)
- var tra: Boolean = config("TRA", default = true)
-
- override def init(): Unit = {
- if (outputName == null) outputName = input.getName.stripSuffix(".bam")
- if (outputVcf == null) outputVcf = new File(workDir, outputName + ".delly.vcf")
- }
-
- def biopetScript() {
- // write the pipeline here
- logger.info("Configuring Delly pipeline")
- var outputFiles: Map[String, File] = Map()
- var vcfFiles: Map[String, File] = Map()
-
- /// start delly and then copy the vcf into the root directory "<sample>.delly/"
- if (del) {
- val delly = new DellyCaller(this)
- delly.input = input
- delly.analysistype = "DEL"
- delly.outputvcf = new File(workDir, outputName + ".delly.del.vcf")
- add(delly)
- vcfFiles += ("DEL" -> delly.outputvcf)
- }
- if (dup) {
- val delly = new DellyCaller(this)
- delly.input = input
- delly.analysistype = "DUP"
- delly.outputvcf = new File(workDir, outputName + ".delly.dup.vcf")
- add(delly)
- vcfFiles += ("DUP" -> delly.outputvcf)
- }
- if (inv) {
- val delly = new DellyCaller(this)
- delly.input = input
- delly.analysistype = "INV"
- delly.outputvcf = new File(workDir, outputName + ".delly.inv.vcf")
- add(delly)
- vcfFiles += ("INV" -> delly.outputvcf)
- }
- if (tra) {
- val delly = new DellyCaller(this)
- delly.input = input
- delly.analysistype = "TRA"
- delly.outputvcf = new File(workDir, outputName + ".delly.tra.vcf")
- // vcfFiles += ("TRA" -> delly.outputvcf)
- add(delly)
- }
- // we need to merge the vcf's
- val finalVCF = if (vcfFiles.size > 1) {
- // do merging
- // CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
- //TODO: convert to biopet extension
- val variants = new CatVariants()
- variants.variant = vcfFiles.values.toList
- variants.outputFile = this.outputVcf
- variants.reference = referenceFasta()
- // add the job
- //add(variants)
- Some(outputVcf)
- } else if (vcfFiles.size == 1) {
- // TODO: pretify this
- val ln = Ln(this, vcfFiles.head._2, this.outputVcf, relative = true)
- //add(ln)
- Some(ln.output)
- } else None
-
- finalVCF.foreach(file => outputFiles += ("vcf" -> file))
- }
-}
-
-object Delly extends PipelineCommand {
- override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
-
- def apply(root: Configurable, input: File, workDir: File): Delly = {
- val dellyPipeline = new Delly(root)
- dellyPipeline.input = input
- dellyPipeline.workDir = workDir
- dellyPipeline.init()
- dellyPipeline.biopetScript()
- dellyPipeline
- }
-
-}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
new file mode 100644
index 0000000000000000000000000000000000000000..d5e3fffcfaeb7d842743ecc9e8896e7de860bbed
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
@@ -0,0 +1,55 @@
+/**
+ * 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.gatk
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
+
+ javaMainClass = classOf[org.broadinstitute.gatk.tools.CatVariants].getClass.getName
+
+ @Input(required = true)
+ var inputFiles: List[File] = Nil
+
+ @Output(required = true)
+ var outputFile: File = null
+
+ @Input
+ var reference: File = null
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ if (reference == null) reference = referenceFasta()
+ }
+
+ override def cmdLine = super.cmdLine +
+ repeat("-V", inputFiles) +
+ required("-out", outputFile) +
+ required("-R", reference)
+}
+
+object CatVariants {
+ def apply(root: Configurable, input: List[File], output: File): CatVariants = {
+ val cv = new CatVariants(root)
+ cv.inputFiles = input
+ cv.outputFile = output
+ cv
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
index 8291e667b67df0b03a10114f6386670f18d572e4..cc230a6ad48e50f782f773a54d1537a72ad85e2d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
@@ -49,6 +49,7 @@ class CombineVariants(val root: Configurable) extends Gatk {
override def beforeGraph(): Unit = {
super.beforeGraph()
+ if (outputFile.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputFile.getAbsolutePath + ".tbi")
genotypeMergeOptions match {
case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None =>
case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
similarity index 98%
rename from protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index 11b59f2fa52bf56e455475e2e719a746f6ff41ed..f4efc801d2ee4d60c6ffb949dd602334a8491836 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
@@ -10,8 +10,6 @@ import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
- memoryLimit = Option(3)
-
var executable: String = config("java", default = "java", submodule = "java", freeVar = false)
override def subPath = "gatk" :: super.subPath
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 0479bbb754d62a13e4e7d99bf6ac949b8cd69aec..087614a6a81367d6826e6d65ffa97d4610e3cd5d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
@Output(doc = "Output chart", required = false)
var outputChart: File = _
- @Output(doc = "Output summary", required = false)
+ @Output(doc = "Output summary", required = true)
var outputSummary: File = _
@Input(doc = "Reference file", required = false)
@@ -67,7 +67,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
required("OUTPUT=", output, spaceSeparated = false) +
optional("CHART_OUTPUT=", outputChart, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", reference, spaceSeparated = false) +
- optional("SUMMARY_OUTPUT=", outputSummary, spaceSeparated = false) +
+ required("SUMMARY_OUTPUT=", outputSummary, spaceSeparated = false) +
optional("WINDOW_SIZE=", windowSize, spaceSeparated = false) +
optional("MINIMUM_GENOME_FRACTION=", minGenomeFraction, spaceSeparated = false) +
conditional(assumeSorted, "ASSUME_SORTED=TRUE") +
@@ -86,6 +86,7 @@ object CollectGcBiasMetrics {
val collectGcBiasMetrics = new CollectGcBiasMetrics(root)
collectGcBiasMetrics.input :+= input
collectGcBiasMetrics.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".gcbiasmetrics")
+ collectGcBiasMetrics.outputSummary = new File(outputDir, input.getName.stripSuffix(".bam") + ".gcbiasmetrics.summary")
collectGcBiasMetrics
}
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
index b1f545fb321f79ab2b5605a6e454dee0586ff2eb..f0703990369edb6791ffb11b61bdbbf0927a270a 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
/** General class for samtools extensions */
abstract class Samtools extends BiopetCommandLineFunction with Version {
override def subPath = "samtools" :: super.subPath
- executable = config("exe", default = "samtools")
+ executable = config("exe", default = "samtools", submodule = "samtools", freeVar = false)
def versionCommand = executable
def versionRegex = """Version: (.*)""".r
override def versionExitcode = List(0, 1)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
new file mode 100644
index 0000000000000000000000000000000000000000..08c04857a60297d0aa8c268764d7bff44a3866ac
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
@@ -0,0 +1,28 @@
+/**
+ * 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.vt
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+/**
+ * General vt extension
+ *
+ * Created by pjvan_thof on 1/16/15.
+ */
+abstract class Vt extends BiopetCommandLineFunction {
+ override def subPath = "vt" :: super.subPath
+ executable = config("exe", default = "vt")
+}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
new file mode 100644
index 0000000000000000000000000000000000000000..c5acb62ff24dbf189318122453a8f8db92f24c25
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
@@ -0,0 +1,32 @@
+package nl.lumc.sasc.biopet.extensions.vt
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ Reference, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvanthof on 20/11/15.
+ */
+class VtDecompose(val root: Configurable) extends Vt with Version with Reference {
+ def versionRegex = """decompose (.*)""".r
+ override def versionExitcode = List(0, 1)
+ def versionCommand = executable + " decompose"
+
+ @Input(required = true)
+ var inputVcf: File = _
+
+ @Output(required = true)
+ var outputVcf: File = _
+
+ var intervalsFile: Option[File] = config("intervals_file")
+
+ val smartDecompose: Boolean = config("smart_decompose", default = false)
+
+ def cmdLine = required(executable) + required("decompose") +
+ required("-o", outputVcf) +
+ optional("-I", intervalsFile) +
+ conditional(smartDecompose, "-s") +
+ required(inputVcf)
+}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
new file mode 100644
index 0000000000000000000000000000000000000000..26812e2636a4bd794dc8c74e47c73fb137a3740d
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
@@ -0,0 +1,40 @@
+package nl.lumc.sasc.biopet.extensions.vt
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ Reference, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvanthof on 20/11/15.
+ */
+class VtNormalize(val root: Configurable) extends Vt with Version with Reference {
+ def versionRegex = """normalize (.*)""".r
+ override def versionExitcode = List(0, 1)
+ def versionCommand = executable + " normalize"
+
+ @Input(required = true)
+ var inputVcf: File = _
+
+ @Output(required = true)
+ var outputVcf: File = _
+
+ var windowSize: Option[Int] = config("windows_size")
+
+ var intervalsFile: Option[File] = config("intervals_file")
+
+ var reference: File = _
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ reference = referenceFasta()
+ }
+
+ def cmdLine = required(executable) + required("normalize") +
+ required("-o", outputVcf) +
+ optional("-w", windowSize) +
+ optional("-I", intervalsFile) +
+ required("-r", reference) +
+ required(inputVcf)
+}
\ No newline at end of file
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
index 6dbf83580e16f3c8b19d046142d804052b7ebb80..a7e1ea63f9a07ccdaf62ebd753b8ee5d46b94e27 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
@@ -15,6 +15,7 @@
*/
package nl.lumc.sasc.biopet
+import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutablePublic extends BiopetExecutable {
@@ -34,7 +35,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
def pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
- nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
+ ShivaVariantcalling,
nl.lumc.sasc.biopet.pipelines.basty.Basty
) ::: publicPipelines
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index b6f90cc6261b3677340c51c5d1197a50d901181e..6e7f6c86d0c834b193525aa4261cd4a023217412 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -38,6 +38,9 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
@Output(doc = "Output tag library", shortName = "output", required = true)
var output: File = _
+ @Output
+ private var outputIndex: File = _
+
var minDP: Option[Int] = config("min_dp")
var minAP: Option[Int] = config("min_ap")
var homoFraction: Option[Double] = config("homoFraction")
@@ -50,6 +53,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
override def beforeGraph() {
super.beforeGraph()
if (reference == null) reference = referenceFasta().getAbsolutePath
+ if (output.getName.endsWith(".vcf.gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
val samtoolsMpileup = new SamtoolsMpileup(this)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index 0c2639c7b1bc0e79cae7486a1775f1039d350a15..df131db588a2709d238213968c18aaa86ffb3962 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -30,6 +30,9 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
@Output(doc = "Output vcf", shortName = "o", required = false)
var outputVcf: File = _
+ @Output
+ var outputVcfIndex: File = _
+
var minSampleDepth: Option[Int] = config("min_sample_depth")
var minTotalDepth: Option[Int] = config("min_total_depth")
var minAlternateDepth: Option[Int] = config("min_alternate_depth")
@@ -38,6 +41,11 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
override def defaultCoreMemory = 3.0
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ if (outputVcf.getName.endsWith("vcf.gz")) outputVcfIndex = new File(outputVcf.getAbsolutePath + ".tbi")
+ }
+
override def cmdLine = super.cmdLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 4db2b44745416068a95c0da190a541f9c25479ea..bf52dbea4111a1dfa1227addada89392336a1834 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -54,6 +54,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
var allInfoTags = false
var allGenotypeTags = false
var reference: File = _
+ var intervals: Option[File] = None
override def beforeGraph(): Unit = {
reference = referenceFasta()
@@ -76,7 +77,8 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
repeat("--genotypeTag", genotypeTags) +
conditional(allInfoTags, "--allInfoTags") +
conditional(allGenotypeTags, "--allGenotypeTags") +
- required("-R", reference)
+ required("-R", reference) +
+ optional("--intervals", intervals)
/** Returns general stats to the summary */
def summaryStats: Map[String, Any] = {
diff --git a/public/biopet-utils/pom.xml b/public/biopet-utils/pom.xml
index 6875ae4b93edcc15da0ea333f7cd86be79ffef9c..8b70e105c01ea1fd2eda061129fd4cdc8ae1ff3c 100644
--- a/public/biopet-utils/pom.xml
+++ b/public/biopet-utils/pom.xml
@@ -62,7 +62,7 @@
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
- <version>1.132</version>
+ <version>1.141</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f13230534af0a61fa29f68daa8d48c81a55e1f23
--- /dev/null
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
@@ -0,0 +1,33 @@
+package nl.lumc.sasc.biopet.utils
+
+import java.io.File
+
+import htsjdk.samtools.SamReaderFactory
+
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 11/19/15.
+ */
+object BamUtils {
+
+ /**
+ * This method will convert a list of bam files to a Map[<sampleName>, <bamFile>]
+ *
+ * Each sample may only be once in the list
+ *
+ * @throws IllegalArgumentException
+ * @param bamFiles input bam files
+ * @return
+ */
+ def sampleBamMap(bamFiles: List[File]): Map[String, File] = {
+ val temp = bamFiles.map { file =>
+ val inputSam = SamReaderFactory.makeDefault.open(file)
+ val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
+ if (samples.size == 1) samples.head -> file
+ else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+ }
+ if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
+ temp.toMap
+ }
+}
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index de37b352ecf8a9091ee67d1b455e85087156f642..a31ca43355b72f09d219340725e23d6a0aca2eba 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -150,8 +150,6 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
macs2.name = Some(sampleId)
macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
add(macs2)
-
- addSummaryJobs()
}
}
@@ -176,6 +174,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
logger.info("Starting CArP pipeline")
addSamplesJobs()
+
+ addSummaryJobs()
}
def addMultiSampleJobs(): Unit = {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b34b3772296f9de419f7a249d45daefc513c7259
--- /dev/null
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -0,0 +1,62 @@
+/**
+ * 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.flexiprep
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Cutadapt wrapper specific for Flexiprep.
+ *
+ * This wrapper overrides the summary part so that instead of only displaying the clipped adapters, the sequence names
+ * are also displayed. In Flexiprep the sequence will always have names since they are detected by FastQC from a list
+ * of known adapters / contaminants.
+ *
+ * @param root: Configurable object from which this wrapper is initialized.
+ * @param fastqc: Fastqc wrapper that contains adapter information.
+ */
+class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.extensions.Cutadapt(root) {
+
+ /** Clipped adapter names from FastQC */
+ protected def seqToName = fastqc.foundAdapters
+ .map(adapter => adapter.seq -> adapter.name).toMap
+
+ override def summaryStats: Map[String, Any] = {
+ val initStats = super.summaryStats
+ // Map of adapter sequence and how many times it is found
+ val adapterCounts: Map[String, Any] = initStats.get(adaptersStatsName) match {
+ // "adapters" key found in statistics
+ case Some(m: Map[_, _]) => m.flatMap {
+ case (seq: String, count) =>
+ seqToName.get(seq) match {
+ // adapter sequence is found by FastQC
+ case Some(n) => Some(n -> Map("sequence" -> seq, "count" -> count))
+ // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
+ // sequences come from FastQC
+ case _ =>
+ throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastq_input'.")
+ }
+ // FastQC found no adapters
+ case otherwise =>
+ ;
+ logger.debug(s"No adapters found for summarizing in '$fastq_input'.")
+ None
+ }
+ // "adapters" key not found ~ something went wrong in our part
+ case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastq_input'.")
+ }
+ initStats.updated(adaptersStatsName, adapterCounts)
+ }
+}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 1f1f2510cc600544c95d8db117bad3c3e888be01..7c2b9ace137c347e9f78d99543eb56ebf28ef5b4 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -195,6 +195,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
override def beforeGraph(): Unit = {
fqSync.beforeGraph()
+ commands = qcCmdR1.jobs ::: qcCmdR2.jobs ::: fqSync :: Nil
super.beforeGraph()
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 4cb06039b07e2bbe33fa4396aebc98a022189952..22a9a4a526a0a8d0c640b9262baef99063f07288 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetCommandLineFunction }
-import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle, Cutadapt }
+import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
@@ -50,7 +50,15 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val seqtk = new SeqtkSeq(root)
var clip: Option[Cutadapt] = None
var trim: Option[Sickle] = None
- var outputCommand: BiopetCommandLineFunction = null
+ lazy val outputCommand: BiopetCommandLineFunction = if (compress) {
+ val gzip = Gzip(root)
+ gzip.output = output
+ gzip
+ } else {
+ val cat = Cat(root)
+ cat.output = output
+ cat
+ }
def jobs = (Some(seqtk) :: clip :: trim :: Some(outputCommand) :: Nil).flatten
@@ -93,7 +101,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
clip = if (!flexiprep.skipClip) {
val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (foundAdapters.nonEmpty) {
- val cutadapt = new Cutadapt(root)
+ val cutadapt = new Cutadapt(root, fastqc)
cutadapt.fastq_input = seqtk.output
cutadapt.fastq_output = new File(output.getParentFile, input.getName + ".cutadapt.fq")
cutadapt.stats_output = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
@@ -123,16 +131,9 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case _ => seqtk.output
}
- if (compress) outputCommand = {
- val gzip = new Gzip(root)
- gzip.output = output
- outputFile :<: gzip
- }
- else outputCommand = {
- val cat = new Cat(root)
- cat.input = outputFile :: Nil
- cat.output = output
- cat
+ outputCommand match {
+ case gzip: Gzip => outputFile :<: gzip
+ case cat: Cat => cat.input = outputFile :: Nil
}
seqtk.beforeGraph()
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
index 8bc095e84ac3d566d3b0f453ecb0eeccd93f553e..674910dabedc3fcb7d7759cd8952d93a68240f01 100644
--- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
@@ -8,13 +8,20 @@
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
-<%@ var showIntro: Boolean = true%>
+<%@ var showIntro: Boolean = true %>
+<%@ var target: Option[String] = None %>
+<%@ var caller: String = "final" %>
+
#{
val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
+ val vcfstatsKey = target match {
+ case Some(t) => s"multisample-vcfstats-$caller-$t"
+ case _ => s"multisample-vcfstats-$caller"
+ }
}#
#if (showIntro)
@@ -70,7 +77,7 @@
#for (sample <- samples.toList.sorted)
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (field <- fields)
- <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
+ <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", vcfstatsKey, "genotype", field)}</td>
#end
</tr>
#end
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index e09b34e74fc290034b2238a9a64fb49826ec029e..5c88189833b1b6bd169c3da475c6c2370957abf9 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -107,11 +107,14 @@ object ShivaReport extends MultisampleReportBuilder {
}
if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
- List(),
- regionPages.map(p => p._1 -> ReportSection(
- "/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp",
- Map("target" -> p._1.stripSuffix(" (Amplicon)"))
+ regionPages.map(p => p._1 -> ReportPage(Nil,
+ List(
+ "Variants" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp", Map("showPlot" -> true)),
+ "Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")
+ ),
+ Map("target" -> Some(p._1.stripSuffix(" (Amplicon)")))
)).toList.sortBy(_._1),
+ List(),
Map())
)
else None
@@ -178,7 +181,9 @@ object ShivaReport extends MultisampleReportBuilder {
prefix: String,
summary: Summary,
libraryLevel: Boolean = false,
- sampleId: Option[String] = None): Unit = {
+ sampleId: Option[String] = None,
+ caller: String = "final",
+ target: Option[String] = None): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
@@ -186,14 +191,14 @@ object ShivaReport extends MultisampleReportBuilder {
tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")
def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
- val homVar = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomVar"),
- summary, Some(sample), lib).value.getOrElse(0).toString.toLong
- val homRef = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomRef"),
- summary, Some(sample), lib).value.getOrElse(0).toString.toLong
- val noCall = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "NoCall"),
- summary, Some(sample), lib).value.getOrElse(0).toString.toLong
- val het = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "Het"),
- summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val path = target match {
+ case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
+ case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
+ }
+ val homVar = new SummaryValue(path :+ "HomVar", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val homRef = new SummaryValue(path :+ "HomRef", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val noCall = new SummaryValue(path :+ "NoCall", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val het = new SummaryValue(path :+ "Het", 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(homVar + "\t")
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
index 79a5219751a35691885b4f61365f4d71b0333105..a810b5257a94479e5e7125e6755722543457ec30 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
@@ -15,18 +15,13 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
-import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
-import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
-import scala.collection.JavaConversions._
-
/**
* Common trait for ShivaVariantcalling
*
@@ -40,25 +35,11 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
@Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
protected var inputBamsArg: List[File] = Nil
- protected var inputBams: Map[String, File] = Map()
-
- def addBamFile(file: File, sampleId: Option[String] = None): Unit = {
- sampleId match {
- case Some(sample) => inputBams += sample -> file
- case _ if !file.exists() => throw new IllegalArgumentException("Bam file does not exits: " + file)
- case _ => {
- val inputSam = SamReaderFactory.makeDefault.open(file)
- val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
- if (samples.size == 1) {
- inputBams += samples.head -> file
- } else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
- }
- }
- }
+ var inputBams: Map[String, File] = Map()
/** Executed before script */
def init(): Unit = {
- inputBamsArg.foreach(addBamFile(_))
+ if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
}
/** Variantcallers requested by the config */
@@ -76,68 +57,16 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
- callers.foreach(_.addJobs())
+ callers.foreach { caller =>
+ caller.outputDir = new File(outputDir, caller.name)
+ add(caller)
+ }
addSummaryJobs()
}
/** Will generate all available variantcallers */
- protected def callersList: List[SvCaller] = List(new Breakdancer, new Clever, new Delly)
-
- /** General trait for a variantcaller mode */
- trait SvCaller {
- /** Name of mode, this should also be used in the config */
- val name: String
-
- /** Output dir for this mode */
- def outputDir = new File(qscript.outputDir, name)
-
- /** This should add the variantcaller jobs */
- def addJobs()
- }
-
- /** default mode of freebayes */
- class Breakdancer extends SvCaller {
- val name = "breakdancer"
-
- def addJobs() {
- //TODO: move minipipeline of breakdancer to here
- for ((sample, bamFile) <- inputBams) {
- val breakdancerDir = new File(outputDir, sample)
- val breakdancer = Breakdancer(qscript, bamFile, breakdancerDir)
- addAll(breakdancer.functions)
- }
- }
- }
-
- /** default mode of bcftools */
- class Clever extends SvCaller {
- val name = "clever"
-
- def addJobs() {
- //TODO: check double directories
- for ((sample, bamFile) <- inputBams) {
- val cleverDir = new File(outputDir, sample)
- val clever = CleverCaller(qscript, bamFile, cleverDir)
- add(clever)
- }
- }
- }
-
- /** Makes a vcf file from a mpileup without statistics */
- class Delly extends SvCaller {
- val name = "delly"
-
- def addJobs() {
- //TODO: Move mini delly pipeline to here
- for ((sample, bamFile) <- inputBams) {
- val dellyDir = new File(outputDir, sample)
- val delly = Delly(qscript, bamFile, dellyDir)
- delly.outputName = sample
- addAll(delly.functions)
- }
- }
- }
+ protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this))
/** Location of summary file */
def summaryFile = new File(outputDir, "ShivaSvCalling.summary.json")
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 5c243df8660bfc0e3333e21dff782e9fc404c5ad..ca2706f710c23ae1625d2908bdc914a2a687afb2 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
@@ -15,16 +15,15 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
-import java.io.File
-
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, Reference }
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.bammetrics.{ TargetRegions, BamMetrics }
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.queue.QScript
import scala.collection.JavaConversions._
@@ -33,8 +32,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 2/26/15.
*/
-trait ShivaTrait extends MultiSampleQScript with Reference {
- qscript =>
+trait ShivaTrait extends MultiSampleQScript with Reference with TargetRegions { qscript: QScript =>
/** Executed before running the script */
def init(): Unit = {
@@ -233,8 +231,8 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
vc.sampleId = Some(sampleId)
vc.libId = Some(libId)
vc.outputDir = new File(libDir, "variantcalling")
- if (preProcessBam.isDefined) vc.inputBams = preProcessBam.get :: Nil
- else vc.inputBams = bamFile.get :: Nil
+ if (preProcessBam.isDefined) vc.inputBams = Map(sampleId -> preProcessBam.get)
+ else vc.inputBams = Map(sampleId -> bamFile.get)
vc.init()
vc.biopetScript()
addAll(vc.functions)
@@ -299,7 +297,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
variantcalling.foreach(vc => {
vc.sampleId = Some(sampleId)
vc.outputDir = new File(sampleDir, "variantcalling")
- vc.inputBams = bam :: Nil
+ vc.inputBams = Map(sampleId -> bam)
vc.init()
vc.biopetScript()
addAll(vc.functions)
@@ -326,7 +324,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
def addMultiSampleJobs(): Unit = {
multisampleVariantCalling.foreach(vc => {
vc.outputDir = new File(outputDir, "variantcalling")
- vc.inputBams = samples.flatMap(_._2.preProcessBam).toList
+ vc.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
vc.init()
vc.biopetScript()
addAll(vc.functions)
@@ -344,7 +342,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
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.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
sv.init()
sv.biopetScript()
addAll(sv.functions)
@@ -356,19 +354,14 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
def summaryFile = new File(outputDir, "Shiva.summary.json")
/** Settings of pipeline for summary */
- def summarySettings = {
- val roiBedFiles: List[File] = config("regions_of_interest", Nil)
- val ampliconBedFile: Option[File] = config("amplicon_bed")
-
- Map(
- "reference" -> referenceSummary,
- "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
- "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed")),
- "annotation" -> annotation.isDefined,
- "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
- "sv_calling" -> svCalling.isDefined
- )
- }
+ def summarySettings = Map(
+ "reference" -> referenceSummary,
+ "annotation" -> annotation.isDefined,
+ "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
+ "sv_calling" -> svCalling.isDefined,
+ "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
+ "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+ )
/** Files for the summary */
def summaryFiles = Map("referenceFasta" -> referenceFasta())
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 6eb2832c17acea6bcdc0d6766d48d3100dc73472..31ba0a53f0fc034b406cca237656722ca9de9d6f 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
@@ -15,28 +15,37 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
-import java.io.File
-
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
-import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeConcordance, CombineVariants }
-import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.extensions.{ Ln, Bgzip, Tabix }
-import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.utils.commandline.Input
+import nl.lumc.sasc.biopet.extensions.Tabix
+import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
+import org.broadinstitute.gatk.queue.QScript
/**
* Common trait for ShivaVariantcalling
*
* Created by pjvan_thof on 2/26/15.
*/
-trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with Reference {
- qscript =>
+trait ShivaVariantcallingTrait extends SummaryQScript
+ with SampleLibraryTag
+ with Reference
+ with TargetRegions {
+ qscript: QScript =>
@Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
- var inputBams: List[File] = Nil
+ protected var inputBamsArg: List[File] = Nil
+
+ var inputBams: Map[String, File] = Map()
+
+ /** Executed before script */
+ def init(): Unit = {
+ if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
+ }
var referenceVcf: Option[File] = config("reference_vcf")
@@ -53,25 +62,22 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
override def defaults = Map("bcftoolscall" -> Map("f" -> List("GQ")))
- /** Executed before script */
- def init(): Unit = {
- }
-
/** Final merged output files of all variantcaller modes */
def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
/** Variantcallers requested by the config */
protected val configCallers: Set[String] = config("variantcallers")
+ protected val callers: List[Variantcaller] = {
+ (for (name <- configCallers) yield {
+ if (!callersList.exists(_.name == name))
+ Logging.addError(s"variantcaller '$name' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+ callersList.find(_.name == name)
+ }).flatten.toList.sortBy(_.prio)
+ }
+
/** This will add jobs for this pipeline */
def biopetScript(): Unit = {
- for (cal <- configCallers) {
- if (!callersList.exists(_.name == cal))
- Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
- }
-
- val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
-
require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + callersList.map(_.name).mkString(", "))
@@ -81,215 +87,89 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
cv.genotypeMergeOptions = Some("PRIORITIZE")
cv.rodPriorityList = callers.map(_.name).mkString(",")
for (caller <- callers) {
- caller.addJobs()
- cv.addInput(caller.outputFile, caller.name)
-
- val vcfStats = new VcfStats(qscript)
- vcfStats.input = caller.outputFile
- vcfStats.setOutputDir(new File(caller.outputDir, "vcfstats"))
- add(vcfStats)
- addSummarizable(vcfStats, namePrefix + "-vcfstats-" + caller.name)
-
- referenceVcf.foreach(referenceVcfFile => {
- val gc = new GenotypeConcordance(this)
- gc.evalFile = caller.outputFile
- gc.compFile = referenceVcfFile
- gc.outputFile = new File(caller.outputDir, s"$namePrefix-genotype_concordance.${caller.name}.txt")
- referenceVcfRegions.foreach(gc.intervals ::= _)
- add(gc)
- addSummarizable(gc, s"$namePrefix-genotype_concordance-${caller.name}")
- })
+ caller.inputBams = inputBams
+ caller.namePrefix = namePrefix
+ caller.outputDir = new File(outputDir, caller.name)
+ add(caller)
+ addStats(caller.outputFile, caller.name)
+ val normalize: Boolean = config("execute_vt_normalize", default = false, submodule = caller.configName)
+ val decompose: Boolean = config("execute_vt_decompose", default = false, submodule = caller.configName)
+
+ val vtNormalize = new VtNormalize(this)
+ vtNormalize.inputVcf = caller.outputFile
+ val vtDecompose = new VtDecompose(this)
+
+ if (normalize && decompose) {
+ vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
+ vtNormalize.isIntermediate = true
+ add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
+ vtDecompose.inputVcf = vtNormalize.outputVcf
+ vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
+ add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
+ cv.addInput(vtDecompose.outputVcf, caller.name)
+ } else if (normalize && !decompose) {
+ vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
+ add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
+ cv.addInput(vtNormalize.outputVcf, caller.name)
+ } else if (!normalize && decompose) {
+ vtDecompose.inputVcf = caller.outputFile
+ vtDecompose.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".decompose.vcf.gz")
+ add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
+ cv.addInput(vtDecompose.outputVcf, caller.name)
+ } else cv.addInput(caller.outputFile, caller.name)
}
add(cv)
+ addStats(finalFile, "final")
+
+ addSummaryJobs()
+ }
+
+ protected def addStats(vcfFile: File, name: String): Unit = {
val vcfStats = new VcfStats(qscript)
- vcfStats.input = finalFile
- vcfStats.setOutputDir(new File(outputDir, "vcfstats"))
- vcfStats.infoTags :+= cv.setKey
+ vcfStats.input = vcfFile
+ vcfStats.setOutputDir(new File(vcfFile.getParentFile, "vcfstats"))
+ if (name == "final") vcfStats.infoTags :+= "VariantCaller"
add(vcfStats)
- addSummarizable(vcfStats, namePrefix + "-vcfstats-final")
+ addSummarizable(vcfStats, s"$namePrefix-vcfstats-$name")
referenceVcf.foreach(referenceVcfFile => {
val gc = new GenotypeConcordance(this)
- gc.evalFile = finalFile
+ gc.evalFile = vcfFile
gc.compFile = referenceVcfFile
- gc.outputFile = new File(outputDir, s"$namePrefix-genotype_concordance.final.txt")
+ gc.outputFile = new File(vcfFile.getParentFile, s"$namePrefix-genotype_concordance.$name.txt")
referenceVcfRegions.foreach(gc.intervals ::= _)
add(gc)
- addSummarizable(gc, s"$namePrefix-genotype_concordance-final")
+ addSummarizable(gc, s"$namePrefix-genotype_concordance-$name")
})
- addSummaryJobs()
- }
-
- /** Will generate all available variantcallers */
- protected def callersList: List[Variantcaller] = List(new Freebayes, new RawVcf, new Bcftools, new BcftoolsSingleSample)
-
- /** General trait for a variantcaller mode */
- trait Variantcaller {
- /** Name of mode, this should also be used in the config */
- val name: String
-
- /** Output dir for this mode */
- def outputDir = new File(qscript.outputDir, name)
-
- /** Prio in merging in the final file */
- protected val defaultPrio: Int
-
- /** Prio from the config */
- lazy val prio: Int = config("prio_" + name, default = defaultPrio)
-
- /** This should add the variantcaller jobs */
- def addJobs()
-
- /** Final output file of this mode */
- def outputFile: File
- }
-
- /** default mode of freebayes */
- class Freebayes extends Variantcaller {
- val name = "freebayes"
- protected val defaultPrio = 7
-
- /** Final output file of this mode */
- def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf.gz")
-
- def addJobs() {
- val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(qscript)
- fb.bamfiles = inputBams
- fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
- fb.isIntermediate = true
- add(fb)
-
- //TODO: need piping for this, see also issue #114
- val bz = new Bgzip(qscript)
- bz.input = List(fb.outputVcf)
- bz.output = outputFile
- add(bz)
-
- val ti = new Tabix(qscript)
- ti.input = bz.output
- ti.p = Some("vcf")
- add(ti)
- }
- }
-
- /** default mode of bcftools */
- class Bcftools extends Variantcaller {
- val name = "bcftools"
- protected val defaultPrio = 8
-
- /** Final output file of this mode */
- def outputFile = new File(outputDir, namePrefix + ".bcftools.vcf.gz")
-
- def addJobs() {
- val mp = new SamtoolsMpileup(qscript)
- mp.input = inputBams
- mp.u = true
- mp.reference = referenceFasta()
-
- val bt = new BcftoolsCall(qscript)
- bt.O = Some("z")
- bt.v = true
- bt.c = true
-
- add(mp | bt > outputFile)
- add(Tabix(qscript, outputFile))
- }
- }
-
- /** default mode of bcftools */
- class BcftoolsSingleSample extends Variantcaller {
- val name = "bcftools_singlesample"
- protected val defaultPrio = 8
-
- /** Final output file of this mode */
- def outputFile = new File(outputDir, namePrefix + ".bcftools_singlesample.vcf.gz")
-
- def addJobs() {
- val sampleVcfs = for (inputBam <- inputBams) yield {
- val mp = new SamtoolsMpileup(qscript)
- mp.input :+= inputBam
- mp.u = true
- mp.reference = referenceFasta()
-
- val bt = new BcftoolsCall(qscript)
- bt.O = Some("z")
- bt.v = true
- bt.c = true
- bt.output = new File(outputDir, inputBam.getName + ".vcf.gz")
-
- add(mp | bt)
- add(Tabix(qscript, bt.output))
- bt.output
- }
-
- if (sampleVcfs.size > 1) {
- val bcfmerge = new BcftoolsMerge(qscript)
- bcfmerge.input = sampleVcfs
- bcfmerge.output = outputFile
- bcfmerge.O = Some("z")
- add(bcfmerge)
- } else add(Ln.apply(qscript, sampleVcfs.head, outputFile))
- add(Tabix(qscript, outputFile))
+ for (bedFile <- ampliconBedFile.toList ::: roiBedFiles) {
+ val regionName = bedFile.getName.stripSuffix(".bed")
+ val vcfStats = new VcfStats(qscript)
+ vcfStats.input = vcfFile
+ vcfStats.intervals = Some(bedFile)
+ vcfStats.setOutputDir(new File(vcfFile.getParentFile, s"vcfstats-$regionName"))
+ if (name == "final") vcfStats.infoTags :+= "VariantCaller"
+ add(vcfStats)
+ addSummarizable(vcfStats, s"$namePrefix-vcfstats-$name-$regionName")
}
}
- /** Makes a vcf file from a mpileup without statistics */
- class RawVcf extends Variantcaller {
- val name = "raw"
-
- // This caller is designed as fallback when other variantcallers fails to report
- protected val defaultPrio = Int.MaxValue
-
- /** Final output file of this mode */
- def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
-
- def addJobs() {
- val rawFiles = inputBams.map(bamFile => {
- val mp = new SamtoolsMpileup(qscript) {
- override def configName = "samtoolsmpileup"
- override def defaults = Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
- }
- mp.input :+= bamFile
-
- val m2v = new MpileupToVcf(qscript)
- m2v.inputBam = bamFile
- m2v.output = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.vcf")
- add(mp | m2v)
-
- val vcfFilter = new VcfFilter(qscript) {
- override def configName = "vcffilter"
- override def defaults = Map("min_sample_depth" -> 8,
- "min_alternate_depth" -> 2,
- "min_samples_pass" -> 1,
- "filter_ref_calls" -> true
- )
- }
- vcfFilter.inputVcf = m2v.output
- vcfFilter.outputVcf = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.filter.vcf.gz")
- add(vcfFilter)
- vcfFilter.outputVcf
- })
-
- val cv = new CombineVariants(qscript)
- cv.inputFiles = rawFiles
- cv.outputFile = outputFile
- cv.setKey = "null"
- cv.excludeNonVariants = true
- add(cv)
- }
- }
+ /** Will generate all available variantcallers */
+ protected def callersList: List[Variantcaller] = List(new Freebayes(this), new RawVcf(this), new Bcftools(this), new BcftoolsSingleSample(this))
/** Location of summary file */
def summaryFile = new File(outputDir, "ShivaVariantcalling.summary.json")
/** Settings for the summary */
- def summarySettings = Map("variantcallers" -> configCallers.toList)
+ def summarySettings = Map(
+ "variantcallers" -> configCallers.toList,
+ "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
+ "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+ )
/** Files for the summary */
def summaryFiles: Map[String, File] = {
- val callers: Set[String] = config("variantcallers")
- callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
+ callers.map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
}
}
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
new file mode 100644
index 0000000000000000000000000000000000000000..d7ff2ac12e78f7e149a3beea14eaea766d385079
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
@@ -0,0 +1,23 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerCaller, BreakdancerConfig }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler Breakdancer */
+class Breakdancer(val root: Configurable) extends SvCaller {
+ def name = "breakdancer"
+
+ def biopetScript() {
+ for ((sample, bamFile) <- inputBams) {
+ val breakdancerSampleDir = new File(outputDir, sample)
+
+ // read config and set all parameters for the pipeline
+ logger.debug("Starting Breakdancer configuration")
+
+ val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
+ val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
+ val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"))
+ add(bdcfg, breakdancer, bdvcf)
+ }
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ff98b32e5f9fe23f6f9e8b52334742b29973da5c
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
@@ -0,0 +1,18 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler Clever */
+class Clever(val root: Configurable) extends SvCaller {
+ def name = "clever"
+
+ def biopetScript() {
+ //TODO: check double directories
+ for ((sample, bamFile) <- inputBams) {
+ val cleverDir = new File(outputDir, sample)
+ val clever = CleverCaller(this, bamFile, cleverDir)
+ add(clever)
+ }
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
new file mode 100644
index 0000000000000000000000000000000000000000..8197f8cc7ea4ff6c72b37e913b8030af17e51151
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
@@ -0,0 +1,60 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
+import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler delly */
+class Delly(val root: Configurable) extends SvCaller {
+ def name = "delly"
+
+ val del: Boolean = config("DEL", default = true)
+ val dup: Boolean = config("DUP", default = true)
+ val inv: Boolean = config("INV", default = true)
+ val tra: Boolean = config("TRA", default = true)
+
+ def biopetScript() {
+ for ((sample, bamFile) <- inputBams) {
+ val dellyDir = new File(outputDir, sample)
+
+ val catVariants = new CatVariants(this)
+ catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz")
+
+ /// start delly and then copy the vcf into the root directory "<sample>.delly/"
+ if (del) {
+ val delly = new DellyCaller(this)
+ delly.input = bamFile
+ delly.analysistype = "DEL"
+ delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
+ add(delly)
+ catVariants.inputFiles :+= delly.outputvcf
+ }
+ if (dup) {
+ val delly = new DellyCaller(this)
+ delly.input = bamFile
+ delly.analysistype = "DUP"
+ delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
+ add(delly)
+ catVariants.inputFiles :+= delly.outputvcf
+ }
+ if (inv) {
+ val delly = new DellyCaller(this)
+ delly.input = bamFile
+ delly.analysistype = "INV"
+ delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
+ add(delly)
+ catVariants.inputFiles :+= delly.outputvcf
+ }
+ if (tra) {
+ val delly = new DellyCaller(this)
+ delly.input = bamFile
+ delly.analysistype = "TRA"
+ delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
+ catVariants.inputFiles :+= delly.outputvcf
+ add(delly)
+ }
+
+ add(catVariants)
+ }
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
new file mode 100644
index 0000000000000000000000000000000000000000..1c63aa7b86954ea2d1fba84473b0cc67eb9a76d0
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
@@ -0,0 +1,19 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 23/11/15.
+ */
+trait SvCaller extends QScript with BiopetQScript with Reference {
+
+ /** Name of mode, this should also be used in the config */
+ def name: String
+
+ var namePrefix: String = _
+
+ var inputBams: Map[String, File] = _
+
+ def init() = {}
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
new file mode 100644
index 0000000000000000000000000000000000000000..fc88e6c212eb8fc4f6dbfb5fbaced0b1a666b195
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Bcftools.scala
@@ -0,0 +1,27 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import nl.lumc.sasc.biopet.extensions.Tabix
+import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** default mode of bcftools */
+class Bcftools(val root: Configurable) extends Variantcaller {
+ val name = "bcftools"
+ protected def defaultPrio = 8
+
+ def biopetScript {
+ val mp = new SamtoolsMpileup(this)
+ mp.input = inputBams.values.toList
+ mp.u = true
+ mp.reference = referenceFasta()
+
+ val bt = new BcftoolsCall(this)
+ bt.O = Some("z")
+ bt.v = true
+ bt.c = true
+
+ add(mp | bt > outputFile)
+ add(Tabix(this, outputFile))
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
new file mode 100644
index 0000000000000000000000000000000000000000..80f0980e3d31cd658c30f93693fa844f0218ef6b
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/BcftoolsSingleSample.scala
@@ -0,0 +1,42 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.extensions.{ Ln, Tabix }
+import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsMerge, BcftoolsCall }
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** default mode of bcftools */
+class BcftoolsSingleSample(val root: Configurable) extends Variantcaller {
+ val name = "bcftools_singlesample"
+ protected def defaultPrio = 8
+
+ def biopetScript {
+ val sampleVcfs = for ((sample, inputBam) <- inputBams.toList) yield {
+ val mp = new SamtoolsMpileup(this)
+ mp.input :+= inputBam
+ mp.u = true
+ mp.reference = referenceFasta()
+
+ val bt = new BcftoolsCall(this)
+ bt.O = Some("z")
+ bt.v = true
+ bt.c = true
+ bt.output = new File(outputDir, sample + ".vcf.gz")
+
+ add(mp | bt)
+ add(Tabix(this, bt.output))
+ bt.output
+ }
+
+ if (sampleVcfs.size > 1) {
+ val bcfmerge = new BcftoolsMerge(this)
+ bcfmerge.input = sampleVcfs
+ bcfmerge.output = outputFile
+ bcfmerge.O = Some("z")
+ add(bcfmerge)
+ } else add(Ln.apply(this, sampleVcfs.head, outputFile))
+ add(Tabix(this, outputFile))
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3227c2dc2fc845fdeb18f3915ae4c692369fdcca
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
@@ -0,0 +1,28 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.extensions.{ Tabix, Bgzip }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** default mode of freebayes */
+class Freebayes(val root: Configurable) extends Variantcaller {
+ val name = "freebayes"
+ protected def defaultPrio = 7
+
+ def biopetScript {
+ val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(this)
+ fb.bamfiles = inputBams.values.toList
+ fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
+ fb.isIntermediate = true
+ add(fb)
+
+ //TODO: need piping for this, see also issue #114
+ val bz = new Bgzip(this)
+ bz.input = List(fb.outputVcf)
+ bz.output = outputFile
+ add(bz)
+
+ add(Tabix.apply(this, bz.output))
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3999ba64b0c8ec36eca933127ca60d8e7da8d201
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
@@ -0,0 +1,52 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.extensions.tools.{ VcfFilter, MpileupToVcf }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Makes a vcf file from a mpileup without statistics */
+class RawVcf(val root: Configurable) extends Variantcaller {
+ val name = "raw"
+
+ // This caller is designed as fallback when other variantcallers fails to report
+ protected def defaultPrio = Int.MaxValue
+
+ def biopetScript {
+ val rawFiles = inputBams.map {
+ case (sample, bamFile) =>
+ val mp = new SamtoolsMpileup(this) {
+ override def configName = "samtoolsmpileup"
+ override def defaults = Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
+ }
+ mp.input :+= bamFile
+
+ val m2v = new MpileupToVcf(this)
+ m2v.inputBam = bamFile
+ m2v.output = new File(outputDir, sample + ".raw.vcf")
+ add(mp | m2v)
+
+ val vcfFilter = new VcfFilter(this) {
+ override def configName = "vcffilter"
+ override def defaults = Map("min_sample_depth" -> 8,
+ "min_alternate_depth" -> 2,
+ "min_samples_pass" -> 1,
+ "filter_ref_calls" -> true
+ )
+ }
+ vcfFilter.inputVcf = m2v.output
+ vcfFilter.outputVcf = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.filter.vcf.gz")
+ add(vcfFilter)
+ vcfFilter.outputVcf
+ }
+
+ val cv = new CombineVariants(this)
+ cv.inputFiles = rawFiles.toList
+ cv.outputFile = outputFile
+ cv.setKey = "null"
+ cv.excludeNonVariants = true
+ add(cv)
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
new file mode 100644
index 0000000000000000000000000000000000000000..eb0a9ffccd11e6bb9d3a4d92af18ba381ce009eb
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
@@ -0,0 +1,29 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 11/19/15.
+ */
+trait Variantcaller extends QScript with BiopetQScript with Reference {
+
+ /** Name of mode, this should also be used in the config */
+ def name: String
+
+ var namePrefix: String = _
+
+ var inputBams: Map[String, File] = _
+
+ def init() = {}
+
+ /** Prio in merging in the final file */
+ protected def defaultPrio: Int
+
+ /** Prio from the config */
+ lazy val prio: Int = config("prio_" + name, default = defaultPrio)
+
+ /** Final output file of this mode */
+ def outputFile: File = new File(outputDir, namePrefix + s".$name.vcf.gz")
+}
+
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 54f5a455364dcd09878667d3a52ca139222190b6..94edda97a3e893ab8bba6d4016f003c2b0242b57 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
@@ -21,7 +21,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.extensions.tools.VcfFilter
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
@@ -72,7 +72,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val map = Map("variantcallers" -> callers.toList)
val pipeline = initPipeline(map)
- pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
+ 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)
diff --git a/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index a0ade5706206c60d9a1a470002c783d0b98a3590..59489d2caa89ac74af08b53c46b781f3e074760d 100644
--- a/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -21,15 +21,15 @@ package nl.lumc.sasc.biopet.pipelines.yamsvp
import java.io.File
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
-import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMarkdup, SambambaMerge }
+import nl.lumc.sasc.biopet.extensions.sambamba.{SambambaMarkdup, SambambaMerge}
+import nl.lumc.sasc.biopet.pipelines.shiva.Delly
+import nl.lumc.sasc.biopet.utils.config.Configurable
//import nl.lumc.sasc.biopet.extensions.pindel.Pindel
-import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import org.broadinstitute.gatk.queue.QScript