From 2261f57e5c2b4cdcd117d810c11c4b01185c3a86 Mon Sep 17 00:00:00 2001 From: hanna Date: Wed, 20 Jan 2010 01:13:17 +0000 Subject: [PATCH] Rename modules to reflect the fact that they're really packages in their own right. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2638 348d0f76-0448-11de-a6fe-93d51630548a --- ...eCovariatesModule.xml => AnalyzeCovariates.xml} | 0 ...sModule.xml => FindContaminatingReadGroups.xml} | 0 packages/GATK-GSA-Pipeline.xml | 14 +++++++------- packages/GATK-Picard.xml | 10 +++++----- packages/GenomeAnalysisTK.xml | 12 ++++++------ ...Module.xml => LocalRealignmentAroundIndels.xml} | 0 ...onModule.xml => QualityScoresRecalibration.xml} | 0 ...iedGenotyperModule.xml => UnifiedGenotyper.xml} | 0 .../{VCFValidatorModule.xml => VCFValidator.xml} | 0 ...antAnnotatorModule.xml => VariantAnnotator.xml} | 0 .../{VariantEvalModule.xml => VariantEval.xml} | 0 ...tFiltrationModule.xml => VariantFiltration.xml} | 0 12 files changed, 18 insertions(+), 18 deletions(-) rename packages/{AnalyzeCovariatesModule.xml => AnalyzeCovariates.xml} (100%) rename packages/{FindContaminatingReadGroupsModule.xml => FindContaminatingReadGroups.xml} (100%) rename packages/{LocalRealignmentAroundIndelsModule.xml => LocalRealignmentAroundIndels.xml} (100%) rename packages/{QualityScoresRecalibrationModule.xml => QualityScoresRecalibration.xml} (100%) rename packages/{UnifiedGenotyperModule.xml => UnifiedGenotyper.xml} (100%) rename packages/{VCFValidatorModule.xml => VCFValidator.xml} (100%) rename packages/{VariantAnnotatorModule.xml => VariantAnnotator.xml} (100%) rename packages/{VariantEvalModule.xml => VariantEval.xml} (100%) rename packages/{VariantFiltrationModule.xml => VariantFiltration.xml} (100%) diff --git a/packages/AnalyzeCovariatesModule.xml b/packages/AnalyzeCovariates.xml similarity index 100% rename from packages/AnalyzeCovariatesModule.xml rename to packages/AnalyzeCovariates.xml diff --git a/packages/FindContaminatingReadGroupsModule.xml b/packages/FindContaminatingReadGroups.xml similarity index 100% rename from packages/FindContaminatingReadGroupsModule.xml rename to packages/FindContaminatingReadGroups.xml diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml index 4d259b64d..155e8d660 100644 --- a/packages/GATK-GSA-Pipeline.xml +++ b/packages/GATK-GSA-Pipeline.xml @@ -7,13 +7,13 @@ GATK-GSA-Pipeline org.broadinstitute.sting.gatk.CommandLineGATK StingText.properties - QualityScoresRecalibrationModule.xml - LocalRealignmentAroundIndelsModule.xml - UnifiedGenotyperModule.xml - VariantFiltrationModule.xml - VariantAnnotatorModule.xml - VariantEvalModule.xml - FindContaminatingReadGroupsModule.xml + QualityScoresRecalibration.xml + LocalRealignmentAroundIndels.xml + UnifiedGenotyper.xml + VariantFiltration.xml + VariantAnnotator.xml + VariantEval.xml + FindContaminatingReadGroups.xml org.broadinstitute.sting.gatk.filters diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml index 0df3a57f1..1dc8c0877 100644 --- a/packages/GATK-Picard.xml +++ b/packages/GATK-Picard.xml @@ -8,11 +8,11 @@ GATK-Picard org.broadinstitute.sting.gatk.CommandLineGATK StingText.properties - QualityScoresRecalibrationModule.xml - LocalRealignmentAroundIndelsModule.xml - UnifiedGenotyperModule.xml - VariantFiltrationModule.xml - VariantAnnotatorModule.xml + QualityScoresRecalibration.xml + LocalRealignmentAroundIndels.xml + UnifiedGenotyper.xml + VariantFiltration.xml + VariantAnnotator.xml org.broadinstitute.sting.gatk.filters diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml index 166cc3355..18ff53388 100644 --- a/packages/GenomeAnalysisTK.xml +++ b/packages/GenomeAnalysisTK.xml @@ -5,12 +5,12 @@ GenomeAnalysisTK org.broadinstitute.sting.gatk.CommandLineGATK StingText.properties - QualityScoresRecalibrationModule.xml - LocalRealignmentAroundIndelsModule.xml - UnifiedGenotyperModule.xml - VariantFiltrationModule.xml - VariantAnnotatorModule.xml - VCFValidatorModule.xml + QualityScoresRecalibration.xml + LocalRealignmentAroundIndels.xml + UnifiedGenotyper.xml + VariantFiltration.xml + VariantAnnotator.xml + VCFValidator.xml org.broadinstitute.sting.gatk.filters diff --git a/packages/LocalRealignmentAroundIndelsModule.xml b/packages/LocalRealignmentAroundIndels.xml similarity index 100% rename from packages/LocalRealignmentAroundIndelsModule.xml rename to packages/LocalRealignmentAroundIndels.xml diff --git a/packages/QualityScoresRecalibrationModule.xml b/packages/QualityScoresRecalibration.xml similarity index 100% rename from packages/QualityScoresRecalibrationModule.xml rename to packages/QualityScoresRecalibration.xml diff --git a/packages/UnifiedGenotyperModule.xml b/packages/UnifiedGenotyper.xml similarity index 100% rename from packages/UnifiedGenotyperModule.xml rename to packages/UnifiedGenotyper.xml diff --git a/packages/VCFValidatorModule.xml b/packages/VCFValidator.xml similarity index 100% rename from packages/VCFValidatorModule.xml rename to packages/VCFValidator.xml diff --git a/packages/VariantAnnotatorModule.xml b/packages/VariantAnnotator.xml similarity index 100% rename from packages/VariantAnnotatorModule.xml rename to packages/VariantAnnotator.xml diff --git a/packages/VariantEvalModule.xml b/packages/VariantEval.xml similarity index 100% rename from packages/VariantEvalModule.xml rename to packages/VariantEval.xml diff --git a/packages/VariantFiltrationModule.xml b/packages/VariantFiltration.xml similarity index 100% rename from packages/VariantFiltrationModule.xml rename to packages/VariantFiltration.xml