64 lines
2.2 KiB
Scala
64 lines
2.2 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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* An introductory pipeline for Queue.
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* Runs the GATK CountReads individually and across a set of bams.
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* All bams must have the same reference.
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*/
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class ExampleCountReads 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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// 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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// Run CountReads for all bams jointly.
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// Create a new CountReads from the Queue GATK Extensions.
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// The names of walkers are the same as you would use for '-T <WalkerName>'
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val jointCountReads = new CountReads
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// Set the GATK jar file for this command.
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jointCountReads.jarFile = gatkJar
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// Each field in the extensions is based off of the full form of the arguments.
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// To get the list of arguments and their descriptions run
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// java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
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jointCountReads.reference_sequence = referenceFile
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// GATK inputs that take more than one file will have a singular name which
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// matches the full form of the argument, but will actually be a scala List[]
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jointCountReads.input_file = bamFiles
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// Add the newly created function to the pipeline.
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add(jointCountReads)
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// If there is more than one BAM, also run CountReads once for each bam.
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if (bamFiles.size > 1) {
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for (bamFile <- bamFiles) {
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val singleCountReads = new CountReads
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singleCountReads.jarFile = gatkJar
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singleCountReads.reference_sequence = referenceFile
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// ':+' is the scala List append operator
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singleCountReads.input_file :+= bamFile
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add(singleCountReads)
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}
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}
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}
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}
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