34 lines
964 B
Scala
34 lines
964 B
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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* An introductory pipeline with integration tests testing the MD5 of the @Output.
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*/
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class ExampleCountLoci extends QScript {
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@Input(doc="The path to the 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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@Input(doc="One or more bam files.", shortName="I")
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var bamFiles: List[File] = Nil
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@Input(doc="Intervals to traverse.", shortName="L", required=false)
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var intervals: List[String] = Nil
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@Output
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var out: File = _
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def script = {
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val countLoci = new CountLoci
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countLoci.jarFile = gatkJar
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countLoci.reference_sequence = referenceFile
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countLoci.input_file = bamFiles
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countLoci.intervalsString = intervals
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countLoci.out = out
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countLoci.memoryLimit = Some(1)
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add(countLoci)
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}
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}
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