104 lines
3.0 KiB
Scala
104 lines
3.0 KiB
Scala
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package org.broadinstitute.sting.queue
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import org.broadinstitute.sting.queue.function.CommandLineFunction
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import org.broadinstitute.sting.queue.engine.QGraph
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/**
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* Syntactic sugar for filling in a pipeline using a Scala script.
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*/
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object QScript {
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// Type aliases so users don't have to import
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type File = java.io.File
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type Input = org.broadinstitute.sting.queue.util.Input
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type Output = org.broadinstitute.sting.queue.util.Output
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type Optional = org.broadinstitute.sting.queue.util.Optional
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type ClassType = org.broadinstitute.sting.queue.util.ClassType
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type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction
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type GatkFunction = org.broadinstitute.sting.queue.function.gatk.GatkFunction
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// The arguments for executing pipelines
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private var qArgs: QArguments = _
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// A default pipeline. Can also use multiple 'new Pipeline()'
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private val pipeline = new Pipeline
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/**
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* Initializes the QArguments and returns a list of the rest of the user args.
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*/
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def setArgs(params: Array[String]) = {
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qArgs = new QArguments(params)
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qArgs.userArgs
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}
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/**
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* Returns a list of files that were specified with "-I <file>" on the command line
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* or inside a .list file.
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*/
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def inputs(extension: String) = qArgs.inputPaths.filter(_.getName.endsWith(extension))
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/**
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* Exchanges the extension on a file.
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*/
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def swapExt(file: File, oldExtension: String, newExtension: String) =
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new File(file.getName.stripSuffix(oldExtension) + newExtension)
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/**
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* Adds one or more command line functions for dispatch later during run()
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*/
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def add(functions: CommandLineFunction*) = pipeline.add(functions:_*)
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/**
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* Sets the @Input and @Output values for all the functions
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*/
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def setParams(): Unit = pipeline.setParams()
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/**
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* Sets the @Input and @Output values for a single function
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*/
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def setParams(function: CommandLineFunction): Unit = pipeline.setParams(function)
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/**
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* Executes functions that have been added to the pipeline.
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*/
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def run() = pipeline.run()
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/**
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* Encapsulates a set of functions to run together.
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*/
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protected class Pipeline {
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private var functions = List.empty[CommandLineFunction]
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/**
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* Adds one or more command line functions for dispatch later during run()
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*/
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def add(functions: CommandLineFunction*) =
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this.functions :::= List(functions:_*)
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/**
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* Sets the @Input and @Output values for all the functions
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*/
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def setParams(): Unit =
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for (function <- functions) setParams(function)
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/**
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* Sets the @Input and @Output values for a single function
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*/
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def setParams(function: CommandLineFunction): Unit =
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for ((name, value) <- qArgs.argMap) function.setValue(name, value)
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/**
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* Executes functions that have been added to the pipeline.
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*/
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def run() = {
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val qGraph = new QGraph
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qGraph.dryRun = qArgs.dryRun
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qGraph.bsubAllJobs = qArgs.bsubAllJobs
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for (function <- functions)
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qGraph.add(function)
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qGraph.fillIn
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qGraph.run
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}
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}
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}
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