Commit 90e96f6c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Path to class for main class changed

parent a2c2e0fc
......@@ -7,7 +7,7 @@ import org.broadinstitute.sting.commandline._
import scala.sys.process._
import scala.util.matching.Regex
trait BiopetCommandLineFunction extends CommandLineFunction {
abstract class BiopetCommandLineFunction extends CommandLineFunction {
val globalConfig: Config
analysisName = getClass.getSimpleName
protected var config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
......
......@@ -267,5 +267,5 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
object Flexiprep extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/flexiprep/"
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.class"
}
......@@ -310,5 +310,5 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
}
object Gatk extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/"
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.class"
}
......@@ -119,51 +119,48 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
}
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
val sortSam = new SortSam {
this.input = inputSam
this.createIndex = true
this.output = outputFile
this.memoryLimit = 2
this.nCoresRequest = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
val sortSam = new SortSam
sortSam.input = inputSam
sortSam.createIndex = true
sortSam.output = outputFile
sortSam.memoryLimit = 2
sortSam.nCoresRequest = 2
sortSam.jobResourceRequests :+= "h_vmem=4G"
add(sortSam)
return sortSam.output
}
def addAddOrReplaceReadGroups(inputSam:List[File], outputFile:File, dir:String) : File = {
val addOrReplaceReadGroups = new AddOrReplaceReadGroups {
this.input = inputSam
this.output = outputFile
this.createIndex = true
this.memoryLimit = 2
this.nCoresRequest = 2
this.jobResourceRequests :+= "h_vmem=4G"
val addOrReplaceReadGroups = new AddOrReplaceReadGroups
addOrReplaceReadGroups.input = inputSam
addOrReplaceReadGroups.output = outputFile
addOrReplaceReadGroups.createIndex = true
addOrReplaceReadGroups.memoryLimit = 2
addOrReplaceReadGroups.nCoresRequest = 2
addOrReplaceReadGroups.jobResourceRequests :+= "h_vmem=4G"
this.RGID = qscript.RGID
this.RGLB = qscript.RGLB
this.RGPL = qscript.RGPL
this.RGPU = qscript.RGPU
this.RGSM = qscript.RGSM
addOrReplaceReadGroups.RGID = qscript.RGID
addOrReplaceReadGroups.RGLB = qscript.RGLB
addOrReplaceReadGroups.RGPL = qscript.RGPL
addOrReplaceReadGroups.RGPU = qscript.RGPU
addOrReplaceReadGroups.RGSM = qscript.RGSM
if (RGCN != null) this.RGCN = qscript.RGCN
if (RGDS != null) this.RGDS = qscript.RGDS
}
add(addOrReplaceReadGroups)
return addOrReplaceReadGroups.output
}
def addMarkDuplicates(input_Bams:List[File], outputFile:File, dir:String) : File = {
val markDuplicates = new MarkDuplicates {
this.input = input_Bams
this.output = outputFile
this.REMOVE_DUPLICATES = false
this.metrics = swapExt(dir,outputFile,".bam",".metrics")
this.outputIndex = swapExt(dir,this.output,".bam",".bai")
this.memoryLimit = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
val markDuplicates = new MarkDuplicates
markDuplicates.input = input_Bams
markDuplicates.output = outputFile
markDuplicates.REMOVE_DUPLICATES = false
markDuplicates.metrics = swapExt(dir,outputFile,".bam",".metrics")
markDuplicates.outputIndex = swapExt(dir,markDuplicates.output,".bam",".bai")
markDuplicates.memoryLimit = 2
markDuplicates.jobResourceRequests :+= "h_vmem=4G"
add(markDuplicates)
return markDuplicates.output
......@@ -200,5 +197,5 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
}
object Mapping extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/"
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
}
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