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the data processing pipeline needs more memory... 

directory updates in the methods pipeline.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5305 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-24 17:22:58 +00:00
parent 897a333aba
commit 6db3210387
2 changed files with 4 additions and 4 deletions
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6
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -109,11 +109,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass),
"HiSeq19" -> new Target("NA12878.HiSeq19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
new File("/humgen/gsa-hpprojects/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass),
"GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
new File("/humgen/gsa-hpprojects/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass),
"WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18_129, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
@ -122,7 +122,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, !lowPass),
"WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),

2
scala/qscript/oneoffs/carneiro/dataProcessing.scala
View File

@ -59,7 +59,7 @@ class dataProcessing extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.GATKjar
this.reference_sequence = qscript.reference
this.memoryLimit = Some(4)
this.memoryLimit = Some(8)
this.isIntermediate = true
}