zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

No more R resources in the DPP 

updating the DPP to conform with Analyze Covariates changes.
This commit is contained in:
Mauricio Carneiro 2011-10-28 16:57:01 -04:00
parent e25d40882a
commit dbd8c25787
1 changed files with 1 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -18,16 +18,13 @@ class DataProcessingPipeline extends QScript {
qscript => qscript =>
/**************************************************************************** /****************************************************************************
* Required Parameters (if default values are not good for you) * Required Parameters
****************************************************************************/ ****************************************************************************/
@Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true) @Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true)
var input: File = _ var input: File = _
@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
var R: String = _
@Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true) @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
var reference: File = _ var reference: File = _
@ -377,7 +374,6 @@ class DataProcessingPipeline extends QScript {
case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates { case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
this.resources = qscript.R
this.recal_file = inRecalFile this.recal_file = inRecalFile
this.output_dir = outPath.toString this.output_dir = outPath.toString
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates" this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"