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updated to work with the new tearsheet 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5113 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-01-28 18:49:11 +00:00
parent bccc71c481
commit b25d131481
1 changed files with 2 additions and 5 deletions
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7
scala/qscript/playground/fullCallingPipeline.q
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@ -411,12 +411,10 @@ class fullCallingPipeline extends QScript {
var bamlist: File =_ var bamlist: File =_
@Input(doc="Eval files root") @Input(doc="Eval files root")
var evalroot: File =_ var evalroot: File =_
@Output(doc="plot pdf loc")
var plots: File =_
@Output(doc="tearsheet loc") @Output(doc="tearsheet loc")
var tearsheet: File =_ var tearsheet: File =_
def commandLine = "Rscript %s -bamlist %s -evalroot %s -tearout %s -plotout %s" def commandLine = "Rscript %s -bamlist %s -evalroot %s -tearout %s"
.format(script, bamlist, evalroot, tearsheet, plots) .format(script, bamlist, evalroot, tearsheet)
} }
val adpr = new rCommand val adpr = new rCommand
@ -425,7 +423,6 @@ class fullCallingPipeline extends QScript {
adpr.evalroot = eval.reportLocation adpr.evalroot = eval.reportLocation
adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out") adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")
adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf") adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf")
adpr.plots = new File("SnpCalls", base + ".plots.pdf")
adpr.analysisName = base + "_ADPR" adpr.analysisName = base + "_ADPR"