50 lines
1.9 KiB
Scala
50 lines
1.9 KiB
Scala
import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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/**
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* A pipeline for Queue that runs a custom walker outside of the GATK jar.
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* NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue.
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* Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
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*/
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class ExampleCustomWalker extends QScript {
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// The full packaged jar should be used.
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// You can build this jar via 'ant package' and then find it under
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// 'Sting/dist/packages/GenomeAnalysisTK-*/GenomeAnalysisTK.jar'
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@Input(doc="The path to the packaged GenomeAnalysisTK.jar file.", shortName="gatk")
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var gatkJar: File = null
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@Input(doc="The reference file for the bam files.", shortName="R")
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var referenceFile: File = null
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// NOTE: Do not initialize List, Set, or Option to null
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// as you won't be able to update the collection.
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// By default set:
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// List[T] = Nil
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// Set[T] = Set.empty[T]
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// Option[T] = None
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@Input(doc="One or more bam files.", shortName="I")
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var bamFiles: List[File] = Nil
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/**
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* In script, you create and then add() functions to the pipeline.
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*/
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def script = {
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val myClasses = "myClassDir"
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val customWalker = new CommandLineGATK {
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// Set the name of your walker, for example this will be passed as -T MyCustomWalker
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this.analysis_type = "MyCustomWalker"
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// NOTE: At this time, you still need to specify the GATK jar or the pipeline won't validate.
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this.jarFile = gatkJar
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override def javaExecutable = "org.broadinstitute.sting.gatk.CommandLineGATK"
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override def javaOpts = "%s -cp %s:%s".format(super.javaOpts, gatkJar, myClasses)
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}
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customWalker.reference_sequence = referenceFile
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customWalker.input_file = bamFiles
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// Add the newly created function to the pipeline.
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add(customWalker)
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}
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}
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