From 4cf7a2af23b638fda353f5babd40e04d3d90e611 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Mon, 18 Jul 2011 23:25:21 -0400 Subject: [PATCH] Removed broad specific default paths so people from outside the broad can use it. --- .../queue/qscripts/RecalibrateBaseQualities.scala | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala index fca420816..f8218148e 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -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