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Removed broad specific default paths so people from outside the broad can use it.

This commit is contained in:
Mauricio Carneiro 2011-07-18 23:25:21 -04:00
parent 1af76736b9
commit 4cf7a2af23
1 changed files with 6 additions and 6 deletions
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12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -20,14 +20,14 @@ class RecalibrateBaseQualities extends QScript {
@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
var input: File = _
@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
@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", shortName="R", required=false)
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="Reference fasta file", shortName="R", required=true)
var reference: File = _ // new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=true)
var dbSNP: File = _ // new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
val queueLogDir: String = ".qlog/"
var nContigs: Int = 0