From b25d1314813eb950c56f9629a74fc16b13a9fcdf Mon Sep 17 00:00:00 2001 From: corin Date: Fri, 28 Jan 2011 18:49:11 +0000 Subject: [PATCH] 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 --- scala/qscript/playground/fullCallingPipeline.q | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/scala/qscript/playground/fullCallingPipeline.q b/scala/qscript/playground/fullCallingPipeline.q index 8d27254b5..6799a47a9 100755 --- a/scala/qscript/playground/fullCallingPipeline.q +++ b/scala/qscript/playground/fullCallingPipeline.q @@ -411,12 +411,10 @@ class fullCallingPipeline extends QScript { var bamlist: File =_ @Input(doc="Eval files root") var evalroot: File =_ - @Output(doc="plot pdf loc") - var plots: File =_ @Output(doc="tearsheet loc") var tearsheet: File =_ - def commandLine = "Rscript %s -bamlist %s -evalroot %s -tearout %s -plotout %s" - .format(script, bamlist, evalroot, tearsheet, plots) + def commandLine = "Rscript %s -bamlist %s -evalroot %s -tearout %s" + .format(script, bamlist, evalroot, tearsheet) } val adpr = new rCommand @@ -425,7 +423,6 @@ class fullCallingPipeline extends QScript { adpr.evalroot = eval.reportLocation adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out") adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf") - adpr.plots = new File("SnpCalls", base + ".plots.pdf") adpr.analysisName = base + "_ADPR"