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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Queue: how to connect GATK walkers?

I am reading through the most recent workshop slides on Queue, and trying to write a scala script to connect the GATK walkers. However, I'm confused how to use the output of last walker as input for the next walker, especially when you have multiple outputs from the last walker. For example, I wrote the following script to connect RealignerTargetCreator and IndelRealigner, and I have a list of bam files as input to RealignerTargetCreator. I don't know whether I should have multiple outputs from RealignerTargetCreator, and how to use the multiple output from RealignerTargetCreator as input for IndelRealigner. My confusion is highlighted as bold comment text below:

def script() {
    val bams = QScriptUtils.createSeqFromFile(qscript.input)

    if (nContigs < 0)
      nContigs = QScriptUtils.getNumberOfContigs(bams(0))
    val baseName = ""
    val outputDir = if (qscript.outputDir.isEmpty()) baseName else qscript.outputDir + "/" + baseName


    val realigner = new RealignerTargetCreator
    realigner.reference_sequence = qscript.referenceFile
    realigner.input_file = bams
    realigner.out = new File(outputDir + "/Realigner")  // **should I have multiple outputs? how do you name individual output files?**

    val indelRealigner = new IndelRealigner
    indelRealigner.input_file :+= realigner.out  // **do I need a for-loop to go through each input files from last walker?**
    indelRealigner.targetIntervals = swapExt(realigner.out, "bam", "intervals")
    indelRealigner.nWayOut = new File(".realigned.bam")

    add(realigner)
    add(indelRealigner)

  }
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