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Fixing the bundle script 

1. someone out there busted it when adding high confidence 1000G calls
2. new path to NA12878 bam
3. updated clashing version argument
This commit is contained in:
Eric Banks 2013-05-02 09:28:40 -04:00
parent 803f666fd5
commit 6d0e383a60
1 changed files with 6 additions and 6 deletions
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12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -40,8 +40,8 @@ class GATKResourcesBundle extends QScript {
@Argument(doc="liftOverPerl", required=false)
var liftOverPerl: File = new File("./public/perl/liftOverVCF.pl")
@Argument(shortName = "ver", doc="The SVN version of this release", required=true)
var VERSION: String = _
@Argument(shortName = "ver", doc="The GIT version of this release", required=true)
var BUNDLE_VERSION: String = _
@Argument(shortName = "bundleDir", doc="Path to root where resource files will be placed", required=false)
val BUNDLE_ROOT = new File("/humgen/gsa-hpprojects/GATK/bundle")
@ -57,8 +57,8 @@ class GATKResourcesBundle extends QScript {
val SITES_EXT: String = "sites"
def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + VERSION
def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + VERSION
def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + BUNDLE_VERSION
def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + BUNDLE_VERSION
// REFERENCES
class Reference( val name: String, val file: File ) { }
@ -161,7 +161,7 @@ class GATKResourcesBundle extends QScript {
"1000G_phase1.indels", b37, true, false))
addResource(new Resource("/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf",
"1000G_phase1.snps.high_confidence, b37, true, false))
"1000G_phase1.snps.high_confidence", b37, true, false))
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf",
"Mills_and_1000G_gold_standard.indels", b37, true, false))
@ -182,7 +182,7 @@ class GATKResourcesBundle extends QScript {
//
// Test BAM file, specific to each reference
//
addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam",
addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.NA12878.bam",
"IGNORE", b37, false, false))
//