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Corrected input/output definitions for Queue 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5173 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-02-02 07:39:00 +00:00
parent 3839fd1a25
commit 7605f0e6c1
1 changed files with 3 additions and 1 deletions
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4
scala/qscript/oneoffs/fromer/PhaseSamples.scala
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@ -34,7 +34,7 @@ class PhaseSamples extends QScript {
@Input(doc = "Samples to phase together. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false) @Input(doc = "Samples to phase together. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
var samplesPerJob = 1 var samplesPerJob = 1
@Input(doc = "Phased file to output", shortName = "o", required = true) @Output(doc = "Phased file to output", shortName = "o", required = true)
var outputPhased: File = _ var outputPhased: File = _
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
@ -154,6 +154,8 @@ class PhaseSamples extends QScript {
class PhasingByACeval() extends org.broadinstitute.sting.queue.extensions.gatk.PhasingEval with CommandLineGATKArgs { class PhasingByACeval() extends org.broadinstitute.sting.queue.extensions.gatk.PhasingEval with CommandLineGATKArgs {
this.analysis = org.broadinstitute.sting.oneoffprojects.walkers.phasing.PhasingEval.Analysis.PHASING_BY_AC this.analysis = org.broadinstitute.sting.oneoffprojects.walkers.phasing.PhasingEval.Analysis.PHASING_BY_AC
this.rodBind :+= RodBind(outputPhased.getName, "VCF", outputPhased)
this.out = new File("phasing_by_ac." + outputPhased + ".txt") this.out = new File("phasing_by_ac." + outputPhased + ".txt")
} }