Commit 2c840f96 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-746

parents 04434f88 08851b43
......@@ -12,14 +12,17 @@
* 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
package nl.lumc.sasc.biopet.extensions.gatk.gather
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
import nl.lumc.sasc.biopet.extensions.picard
import org.broadinstitute.gatk.queue.function.scattergather.{GatherFunction, ScatterGatherableFunction}
/**
* Merges BAM files using htsjdk.samtools.MergeSamFiles.
*
* @deprecated
*/
class MergeSamFiles extends picard.MergeSamFiles(null) with GatherFunction {
......
......@@ -12,7 +12,7 @@
* 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
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
......
......@@ -12,12 +12,13 @@
* 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
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
import org.broadinstitute.gatk.queue.extensions.gatk.GATKIntervals
import org.broadinstitute.gatk.queue.function.scattergather.{ CloneFunction, ScatterFunction }
import org.broadinstitute.gatk.queue.function.scattergather.{CloneFunction, ScatterFunction}
import org.broadinstitute.gatk.utils.commandline.Output
import org.broadinstitute.gatk.utils.interval.IntervalUtils
import org.broadinstitute.gatk.utils.io.IOUtils
......
......@@ -12,7 +12,7 @@
* 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
package nl.lumc.sasc.biopet.extensions.gatk.scatter
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.interval.IntervalUtils
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class GatherBamFiles(val parent: Configurable) extends Picard {
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: List[File] = Nil
var input: Seq[File] = Nil
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
......
/**
* 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 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.picard
import java.io.File
import nl.lumc.sasc.biopet.extensions.Tabix
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class GatherVcfs(val parent: Configurable) extends Picard {
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: Seq[File] = Nil
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
//FIXME: This is a workaround for this issue: https://github.com/broadinstitute/picard/issues/789
def tabix: Option[Tabix] = if (createIndex) Some(Tabix(this, output)) else None
@Output(required = false)
private var index: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
if (createIndex) index = VcfUtils.getVcfIndexFile(output)
}
override def cmdLine: String =
super.cmdLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) + (tabix match {
case Some(t) => s" && ${t.cmdLine}"
case _ => ""
})
}
......@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.CheckValidateVcf
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.gatk._
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.extensions.tools.ValidateVcf
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for the haplotypecaller */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for UnifiedGenotyper */
......
......@@ -20,7 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for GenotyperAllele */
......
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.somatic
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsReheader
import nl.lumc.sasc.biopet.extensions.gatk.{BqsrGather, CombineVariants}
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gatk.gather.BqsrGather
import nl.lumc.sasc.biopet.utils.{IoUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
......
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