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biopet.biopet
Commit 14f35a60 authored by Peter van 't Hof's avatar Peter van 't Hof
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Remove duplicated extensions

parent bf514e93
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala deleted 100644 → 0
View file @ bf514e93
/**
* 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].getName
@Input(required = true)
var inputFiles: List[File] = Nil
@Output(required = true)
var outputFile: File = null
@Input
var reference: File = null
var assumeSorted = false
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) +
conditional(assumeSorted, "--assumeSorted")
}
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
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala deleted 100644 → 0
View file @ bf514e93
/**
* 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.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
/**
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class CombineVariants(val root: Configurable) extends Gatk {
val analysisType = "CombineVariants"
@Input(doc = "", required = true)
var inputFiles: List[File] = Nil
@Output(doc = "", required = true)
var outputFile: File = null
var setKey: String = null
var rodPriorityList: String = null
var minimumN: Int = config("minimumN", default = 1)
var genotypeMergeOptions: Option[String] = config("genotypeMergeOptions")
var excludeNonVariants: Boolean = false
var inputMap: Map[File, String] = Map()
def addInput(file: File, name: String): Unit = {
inputFiles :+= file
inputMap += file -> name
}
@Output
@Gather(enabled = false)
private var outputIndex: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
outputIndex = VcfUtils.getVcfIndexFile(outputFile)
genotypeMergeOptions match {
case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None =>
case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions")
}
deps :::= inputFiles.filter(_.getName.endsWith("vcf.gz")).map(x => new File(x.getAbsolutePath + ".tbi"))
deps = deps.distinct
}
override def cmdLine = super.cmdLine +
(for (file <- inputFiles) yield {
inputMap.get(file) match {
case Some(name) => required("-V:" + name, file)
case _ => required("-V", file)
}
}).mkString +
required("-o", outputFile) +
optional("--setKey", setKey) +
optional("--rod_priority_list", rodPriorityList) +
optional("-genotypeMergeOptions", genotypeMergeOptions) +
conditional(excludeNonVariants, "--excludeNonVariants")
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala deleted 100644 → 0
View file @ bf514e93
/**
* 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.{ Version, BiopetJavaCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.Input
/**
* General extension for GATK module
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
abstract class Gatk extends BiopetJavaCommandLineFunction with Reference with Version {
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar")
val analysisType: String
override def defaultCoreMemory = 3.0
@Input(required = true)
var reference: File = null
@Input(required = false)
var gatkKey: Option[File] = config("gatk_key")
@Input(required = false)
var intervals: List[File] = config("intervals", default = Nil)
@Input(required = false)
var excludeIntervals: List[File] = config("exclude_intervals", default = Nil)
@Input(required = false)
var pedigree: List[File] = config("pedigree", default = Nil)
var et: Option[String] = config("et")
def versionRegex = """(.*)""".r
override def versionExitcode = List(0, 1)
def versionCommand = executable + " -jar " + jarFile + " -version"
override def getVersion = super.getVersion.collect { case version => "Gatk " + version }
override def dictRequired = true
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
}
override def cmdLine = super.cmdLine +
required("-T", analysisType) +
required("-R", reference) +
optional("-K", gatkKey) +
optional("-et", et) +
repeat("-L", intervals) +
repeat("-XL", excludeIntervals) +
repeat("-ped", pedigree)
}
\ No newline at end of file
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala deleted 100644 → 0
View file @ bf514e93
/**
* 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.summary.Summarizable
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.broadinstitute.gatk.utils.report.{ GATKReportTable, GATKReport }
/**
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class GenotypeConcordance(val root: Configurable) extends Gatk with Summarizable {
val analysisType = "GenotypeConcordance"
@Input(required = true)
var evalFile: File = null
@Input(required = true)
var compFile: File = null
@Output(required = true)
var outputFile: File = null
var moltenize = true
def summaryFiles = Map("output" -> outputFile)
def summaryStats = {
val report = new GATKReport(outputFile)
val compProportions = report.getTable("GenotypeConcordance_CompProportions")
val counts = report.getTable("GenotypeConcordance_Counts")
val evalProportions = report.getTable("GenotypeConcordance_EvalProportions")
val genotypeSummary = report.getTable("GenotypeConcordance_Summary")
val siteSummary = report.getTable("SiteConcordance_Summary")
val samples = for (i <- 0 until genotypeSummary.getNumRows) yield genotypeSummary.get(i, "Sample").toString
def getMap(table: GATKReportTable, column: String) = samples.distinct.map(sample => sample -> {
(for (i <- 0 until table.getNumRows if table.get(i, "Sample") == sample) yield s"${table.get(i, "Eval_Genotype")}__${table.get(i, "Comp_Genotype")}" -> table.get(i, column)).toMap
}).toMap
Map(
"compProportions" -> getMap(compProportions, "Proportion"),
"counts" -> getMap(counts, "Count"),
"evalProportions" -> getMap(evalProportions, "Proportion"),
"genotypeSummary" -> samples.distinct.map(sample => {
val i = samples.indexOf(sample)
sample -> Map(
"Non-Reference_Discrepancy" -> genotypeSummary.get(i, "Non-Reference_Discrepancy"),
"Non-Reference_Sensitivity" -> genotypeSummary.get(i, "Non-Reference_Sensitivity"),
"Overall_Genotype_Concordance" -> genotypeSummary.get(i, "Overall_Genotype_Concordance")
)
}).toMap,
"siteSummary" -> Map(
"ALLELES_MATCH" -> siteSummary.get(0, "ALLELES_MATCH"),
"EVAL_SUPERSET_TRUTH" -> siteSummary.get(0, "EVAL_SUPERSET_TRUTH"),
"EVAL_SUBSET_TRUTH" -> siteSummary.get(0, "EVAL_SUBSET_TRUTH"),
"ALLELES_DO_NOT_MATCH" -> siteSummary.get(0, "ALLELES_DO_NOT_MATCH"),
"EVAL_ONLY" -> siteSummary.get(0, "EVAL_ONLY"),
"TRUTH_ONLY" -> siteSummary.get(0, "TRUTH_ONLY")
)
)
}
override def beforeGraph(): Unit = {
super.beforeGraph()
deps :::= (evalFile :: compFile :: Nil).filter(_.getName.endsWith("vcf.gz")).map(x => new File(x.getAbsolutePath + ".tbi"))
deps = deps.distinct
}
override def cmdLine = super.cmdLine +
required("--eval", evalFile) +
required("--comp", compFile) +
required("-o", outputFile) +
conditional(moltenize, "--moltenize")
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala deleted 100644 → 0
View file @ bf514e93
/**
* 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.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
/**
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class SelectVariants(val root: Configurable) extends Gatk {
val analysisType = "SelectVariants"
@Input(doc = "", required = true)
var inputFiles: List[File] = Nil
@Output(doc = "", required = true)
var outputFile: File = null
var excludeNonVariants: Boolean = false
var inputMap: Map[File, String] = Map()
def addInput(file: File, name: String): Unit = {
inputFiles :+= file
inputMap += file -> name
}
@Output
@Gather(enabled = false)
private var outputIndex: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
outputIndex = VcfUtils.getVcfIndexFile(outputFile)
deps :::= inputFiles.filter(_.getName.endsWith("vcf.gz")).map(x => new File(x.getAbsolutePath + ".tbi"))
deps = deps.distinct
}
override def cmdLine = super.cmdLine +
(for (file <- inputFiles) yield {
inputMap.get(file) match {
case Some(name) => required("-V:" + name, file)
case _ => required("-V", file)
}
}).mkString +
required("-o", outputFile) +
conditional(excludeNonVariants, "--excludeNonVariants")
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeConcordance.scala 0 → 100644
View file @ 14f35a60
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.report.{GATKReport, GATKReportTable}
class GenotypeConcordance(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
analysisName = "GenotypeConcordance"
val analysis_type = "GenotypeConcordance"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** The variants and genotypes to evaluate */
@Input(fullName="eval", shortName="eval", doc="The variants and genotypes to evaluate", required=true, exclusiveOf="", validation="")
var eval: File = _
/** The variants and genotypes to compare against */
@Input(fullName="comp", shortName="comp", doc="The variants and genotypes to compare against", required=true, exclusiveOf="", validation="")
var comp: File = _
/** Filters will be ignored */
@Argument(fullName="ignoreFilters", shortName="", doc="Filters will be ignored", required=false, exclusiveOf="", validation="")
var ignoreFilters: Boolean = config("ignoreFilters", default = false)
/** One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod. */
@Argument(fullName="genotypeFilterExpressionEval", shortName="gfe", doc="One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.", required=false, exclusiveOf="", validation="")
var genotypeFilterExpressionEval: List[String] = config("genotypeFilterExpressionEval", default = Nil)
/** One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod. */
@Argument(fullName="genotypeFilterExpressionComp", shortName="gfc", doc="One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.", required=false, exclusiveOf="", validation="")
var genotypeFilterExpressionComp: Seq[String] = config("genotypeFilterExpressionComp", default = Nil)
/** Molten rather than tabular output */
@Argument(fullName="moltenize", shortName="moltenize", doc="Molten rather than tabular output", required=false, exclusiveOf="", validation="")
var moltenize: Boolean = config("moltenize", default = true)
/** File to output the discordant sites and genotypes. */
@Output(fullName="printInterestingSites", shortName="sites", doc="File to output the discordant sites and genotypes.", required=false, exclusiveOf="", validation="")
var printInterestingSites: Option[File] = None
/** An output file created by the walker. Will overwrite contents if file exists */
@Output(fullName="out", shortName="o", doc="An output file created by the walker. Will overwrite contents if file exists", required=false, exclusiveOf="", validation="")
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var out: File = _
/** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
@Argument(fullName="filter_reads_with_N_cigar", shortName="filterRNC", doc="Filter out reads with CIGAR containing the N operator, instead of failing with an error", required=false, exclusiveOf="", validation="")
var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName="filter_mismatching_base_and_quals", shortName="filterMBQ", doc="Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required=false, exclusiveOf="", validation="")
var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName="filter_bases_not_stored", shortName="filterNoBases", doc="Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required=false, exclusiveOf="", validation="")
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
def summaryFiles = Map("output" -> out)
def summaryStats = {
val report = new GATKReport(out)
val compProportions = report.getTable("GenotypeConcordance_CompProportions")
val counts = report.getTable("GenotypeConcordance_Counts")
val evalProportions = report.getTable("GenotypeConcordance_EvalProportions")
val genotypeSummary = report.getTable("GenotypeConcordance_Summary")
val siteSummary = report.getTable("SiteConcordance_Summary")
val samples = for (i <- 0 until genotypeSummary.getNumRows) yield genotypeSummary.get(i, "Sample").toString
def getMap(table: GATKReportTable, column: String) = samples.distinct.map(sample => sample -> {
(for (i <- 0 until table.getNumRows if table.get(i, "Sample") == sample) yield s"${table.get(i, "Eval_Genotype")}__${table.get(i, "Comp_Genotype")}" -> table.get(i, column)).toMap
}).toMap
Map(
"compProportions" -> getMap(compProportions, "Proportion"),
"counts" -> getMap(counts, "Count"),
"evalProportions" -> getMap(evalProportions, "Proportion"),
"genotypeSummary" -> samples.distinct.map(sample => {
val i = samples.indexOf(sample)
sample -> Map(
"Non-Reference_Discrepancy" -> genotypeSummary.get(i, "Non-Reference_Discrepancy"),
"Non-Reference_Sensitivity" -> genotypeSummary.get(i, "Non-Reference_Sensitivity"),
"Overall_Genotype_Concordance" -> genotypeSummary.get(i, "Overall_Genotype_Concordance")
)
}).toMap,
"siteSummary" -> Map(
"ALLELES_MATCH" -> siteSummary.get(0, "ALLELES_MATCH"),
"EVAL_SUPERSET_TRUTH" -> siteSummary.get(0, "EVAL_SUPERSET_TRUTH"),
"EVAL_SUBSET_TRUTH" -> siteSummary.get(0, "EVAL_SUBSET_TRUTH"),
"ALLELES_DO_NOT_MATCH" -> siteSummary.get(0, "ALLELES_DO_NOT_MATCH"),
"EVAL_ONLY" -> siteSummary.get(0, "EVAL_ONLY"),
"TRUTH_ONLY" -> siteSummary.get(0, "TRUTH_ONLY")
)
)
}
override def beforeGraph() {
super.beforeGraph()
if (eval != null) deps :+= VcfUtils.getVcfIndexFile(eval)
if (comp != null) deps :+= VcfUtils.getVcfIndexFile(comp)
}
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-eval", eval), eval, spaceSeparated=true, escape=true, format="%s") +
required(TaggedFile.formatCommandLineParameter("-comp", comp), comp, spaceSeparated=true, escape=true, format="%s") +
conditional(ignoreFilters, "--ignoreFilters", escape=true, format="%s") +
repeat("-gfe", genotypeFilterExpressionEval, spaceSeparated=true, escape=true, format="%s") +
repeat("-gfc", genotypeFilterExpressionComp, spaceSeparated=true, escape=true, format="%s") +
conditional(moltenize, "-moltenize", escape=true, format="%s") +
optional("-sites", printInterestingSites, spaceSeparated=true, escape=true, format="%s") +
optional("-o", out, spaceSeparated=true, escape=true, format="%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape=true, format="%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape=true, format="%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape=true, format="%s")
}
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
View file @ 14f35a60
......@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetQScript, Pipe
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.broad.CombineVariants
import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
......@@ -173,7 +173,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
genomeConfig.get("dbsnp_vcf_uri").foreach { dbsnpUri =>
val cv = new CombineVariants(this)
cv.reference = fastaFile
cv.reference_sequence = fastaFile
cv.deps ::= createDict.output
def addDownload(uri: String): Unit = {
val curl = new Curl(this)
......@@ -181,7 +181,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
curl.output = new File(annotationDir, new File(curl.url).getName)
curl.isIntermediate = true
add(curl)
cv.inputFiles ::= curl.output
cv.variant :+= curl.output
val tabix = new Tabix(this)
tabix.input = curl.output
......@@ -198,7 +198,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
case _ => addDownload(dbsnpUri.toString)
}
cv.outputFile = new File(annotationDir, "dbsnp.vcf.gz")
cv.out = new File(annotationDir, "dbsnp.vcf.gz")
add(cv)
}
......
gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
View file @ 14f35a60
......@@ -6,7 +6,7 @@ import java.util
import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.Snptest
import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.tools.{ GensToVcf, SnptestToVcf }
import nl.lumc.sasc.biopet.pipelines.gwastest.impute.ImputeOutput
import nl.lumc.sasc.biopet.utils.Logging
......@@ -82,10 +82,10 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
gensToVcf.outputVcf = new File(outputDirGens, gen._1.genotypes.getName + s".${gen._2}.vcf.gz")
gensToVcf.isIntermediate = true
add(gensToVcf)
cvChr.inputFiles :+= gensToVcf.outputVcf
cvChr.variant :+= gensToVcf.outputVcf
}
add(cvChr)
cvTotal.inputFiles :+= cvChr.outputFile
cvTotal.variant :+= cvChr.outputFile
contig -> cvChr.outputFile
}
add(cvTotal)
......@@ -105,14 +105,14 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.inputFiles :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
sv.outputFile = new File(regionDir, s"$name.vcf.gz")
sv.variant :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
sv.out = new File(regionDir, s"$name.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
add(sv)
val snptest = new Snptest(this)
snptest.inputGenotypes :+= sv.outputFile
snptest.inputGenotypes :+= sv.out
snptest.inputSampleFiles :+= phenotypeFile
snptest.outputFile = Some(new File(regionDir, s"$name.snptest"))
add(snptest)
......@@ -127,7 +127,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
}
val cv = new CatVariants(this)
cv.inputFiles = snpTests.map(_._2).toList
cv.variant = snpTests.map(_._2).toList
cv.outputFile = new File(outputDir, "snptest" + File.separator + "snptest.vcf.gz")
add(cv)
}
......
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @ 14f35a60
......@@ -15,17 +15,18 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Tabix
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{CombineVariants, GenotypeConcordance}
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
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.{ VarscanCnsSingleSample, _ }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{VarscanCnsSingleSample, _}
import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
/**
* Implementation of ShivaVariantcalling
......@@ -86,10 +87,10 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + callersList.map(_.name).mkString(", "))
val cv = new CombineVariants(qscript)
cv.outputFile = finalFile
cv.out = finalFile
cv.setKey = "VariantCaller"
cv.genotypeMergeOptions = Some("PRIORITIZE")
cv.rodPriorityList = callers.map(_.name).mkString(",")
cv.genotypemergeoption = Some("PRIORITIZE")
cv.rod_priority_list = Some(callers.map(_.name).mkString(","))
for (caller <- callers) {
caller.inputBams = inputBams
caller.namePrefix = namePrefix
......@@ -110,17 +111,17 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
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)
cv.variant :+= TaggedFile(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)