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

Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-05 16:34:21 -04:00
parent a765c08381 5298e3a942
commit 407a0e535f
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/MethodsDevelopmentCallingPipeline.scala
View File

@ -19,10 +19,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
class MethodsDevelopmentCallingPipeline extends QScript {
qscript =>
@Argument(shortName="gatk", doc="gatk jar file", required=true)
var gatkJarFile: File = _
@Argument(shortName="outputDir", doc="output directory", required=true)
@Argument(shortName="outputDir", doc="output directory", required=false)
var outputDir: String = "./"
@Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO";
jarFile = gatkJarFile;
memoryLimit = 4;
phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
}