Commit 695650c2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move aligners to nl.lumc.sasc.biopet.exetensions

parent 14e2e355
......@@ -13,12 +13,13 @@
* 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.aligners
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Fastq file R1", shortName = "R1")
......
......@@ -13,12 +13,13 @@
* 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.aligners
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "FastQ file R1", shortName = "R1")
......
......@@ -13,12 +13,13 @@
* 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.aligners
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class Star(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "The reference file for the bam files.", required = false)
......
......@@ -13,12 +13,13 @@
* 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.aligners
package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "FastQ file R1", shortName = "R1")
......
......@@ -19,8 +19,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.{ Star, Stampy, Bowtie }
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star, Bowtie, Stampy }
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
......@@ -213,7 +214,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
def addBwa(R1: File, R2: File, output: File, deps: List[File]): File = {
val bwaCommand = new Bwa(this)
val bwaCommand = new BwaMem(this)
bwaCommand.R1 = R1
if (paired) bwaCommand.R2 = R2
bwaCommand.deps = deps
......
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