ImputationPipeline --> PRS

broadinstitute · Feb 6, 2025 · c3a7aea · c3a7aea
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diff --git a/ImputationPipeline/AggregatePRSResults.wdl → PRS/AggregatePRSResults.wdl b/ImputationPipeline/AggregatePRSResults.wdl → PRS/AggregatePRSResults.wdl
diff --git a/ImputationPipeline/CKDRiskAdjustment.wdl → PRS/CKDRiskAdjustment.wdl b/ImputationPipeline/CKDRiskAdjustment.wdl → PRS/CKDRiskAdjustment.wdl
diff --git a/...eAggregationSets/CreateAggregationSets.py → ...eAggregationSets/CreateAggregationSets.py b/...eAggregationSets/CreateAggregationSets.py → ...eAggregationSets/CreateAggregationSets.py
diff --git a/...ipeline/CreateAggregationSets/__init__.py → PRS/CreateAggregationSets/__init__.py b/...ipeline/CreateAggregationSets/__init__.py → PRS/CreateAggregationSets/__init__.py
diff --git a/...line/CreateAggregationSets/pyproject.toml → PRS/CreateAggregationSets/pyproject.toml b/...line/CreateAggregationSets/pyproject.toml → PRS/CreateAggregationSets/pyproject.toml
diff --git a/...onSets/tests/CreateAggregationSetsTest.py → ...onSets/tests/CreateAggregationSetsTest.py b/...onSets/tests/CreateAggregationSetsTest.py → ...onSets/tests/CreateAggregationSetsTest.py
diff --git a/...tests/resources/expected_sample_sets.json → ...tests/resources/expected_sample_sets.json b/...tests/resources/expected_sample_sets.json → ...tests/resources/expected_sample_sets.json
diff --git a/...sts/resources/expected_sample_sets_2.json → ...sts/resources/expected_sample_sets_2.json b/...sts/resources/expected_sample_sets_2.json → ...sts/resources/expected_sample_sets_2.json
diff --git a/...ted_sample_sets_2_mix_rework_and_new.json → ...ted_sample_sets_2_mix_rework_and_new.json b/...ted_sample_sets_2_mix_rework_and_new.json → ...ted_sample_sets_2_mix_rework_and_new.json
diff --git a/...expected_sample_sets_2_with_delivery.json → ...expected_sample_sets_2_with_delivery.json b/...expected_sample_sets_2_with_delivery.json → ...expected_sample_sets_2_with_delivery.json
diff --git a/...sts/resources/expected_sample_sets_3.json → ...sts/resources/expected_sample_sets_3.json b/...sts/resources/expected_sample_sets_3.json → ...sts/resources/expected_sample_sets_3.json
diff --git a/...expected_sample_sets_3_with_delivery.json → ...expected_sample_sets_3_with_delivery.json b/...expected_sample_sets_3_with_delivery.json → ...expected_sample_sets_3_with_delivery.json
diff --git a/...sts/resources/expected_sample_sets_4.json → ...sts/resources/expected_sample_sets_4.json b/...sts/resources/expected_sample_sets_4.json → ...sts/resources/expected_sample_sets_4.json
diff --git a/...expected_sample_sets_4_with_delivery.json → ...expected_sample_sets_4_with_delivery.json b/...expected_sample_sets_4_with_delivery.json → ...expected_sample_sets_4_with_delivery.json
diff --git a/...urces/expected_sample_sets_lb_2_only.json → ...urces/expected_sample_sets_lb_2_only.json b/...urces/expected_sample_sets_lb_2_only.json → ...urces/expected_sample_sets_lb_2_only.json
diff --git a/...esources/expected_sample_sets_rework.json → ...esources/expected_sample_sets_rework.json b/...esources/expected_sample_sets_rework.json → ...esources/expected_sample_sets_rework.json
diff --git a/...ources/expected_sample_sets_rework_2.json → ...ources/expected_sample_sets_rework_2.json b/...ources/expected_sample_sets_rework_2.json → ...ources/expected_sample_sets_rework_2.json
diff --git a/...gregationSets/tests/resources/samples.tsv → ...gregationSets/tests/resources/samples.tsv b/...gregationSets/tests/resources/samples.tsv → ...gregationSets/tests/resources/samples.tsv
diff --git a/...regationSets/tests/resources/samples2.tsv → ...regationSets/tests/resources/samples2.tsv b/...regationSets/tests/resources/samples2.tsv → ...regationSets/tests/resources/samples2.tsv
diff --git a/...regationSets/tests/resources/samples3.tsv → ...regationSets/tests/resources/samples3.tsv b/...regationSets/tests/resources/samples3.tsv → ...regationSets/tests/resources/samples3.tsv
diff --git a/...regationSets/tests/resources/samples4.tsv → ...regationSets/tests/resources/samples4.tsv b/...regationSets/tests/resources/samples4.tsv → ...regationSets/tests/resources/samples4.tsv
diff --git a/.../tests/resources/samples_lone_control.tsv → .../tests/resources/samples_lone_control.tsv b/.../tests/resources/samples_lone_control.tsv → .../tests/resources/samples_lone_control.tsv
diff --git a/...s/resources/samples_multiple_controls.tsv → ...s/resources/samples_multiple_controls.tsv b/...s/resources/samples_multiple_controls.tsv → ...s/resources/samples_multiple_controls.tsv
diff --git a/...ts/tests/resources/samples_no_control.tsv → ...ts/tests/resources/samples_no_control.tsv b/...ts/tests/resources/samples_no_control.tsv → ...ts/tests/resources/samples_no_control.tsv
diff --git a/...toverSites/LiftoverSites/LiftoverSites.py → ...toverSites/LiftoverSites/LiftoverSites.py b/...toverSites/LiftoverSites/LiftoverSites.py → ...toverSites/LiftoverSites/LiftoverSites.py
diff --git a/...r/LiftoverSites/LiftoverSites/__init__.py → ...r/LiftoverSites/LiftoverSites/__init__.py b/...r/LiftoverSites/LiftoverSites/__init__.py → ...r/LiftoverSites/LiftoverSites/__init__.py
diff --git a/...ine/Liftover/LiftoverSites/pyproject.toml → PRS/Liftover/LiftoverSites/pyproject.toml b/...ine/Liftover/LiftoverSites/pyproject.toml → PRS/Liftover/LiftoverSites/pyproject.toml
diff --git a/...tationPipeline/ManualQCPRS/ManualQCPRS.py → PRS/ManualQCPRS/ManualQCPRS.py b/...tationPipeline/ManualQCPRS/ManualQCPRS.py → PRS/ManualQCPRS/ManualQCPRS.py
diff --git a/ImputationPipeline/ManualQCPRS/__init__.py → PRS/ManualQCPRS/__init__.py b/ImputationPipeline/ManualQCPRS/__init__.py → PRS/ManualQCPRS/__init__.py
diff --git a/...tationPipeline/ManualQCPRS/pyproject.toml → PRS/ManualQCPRS/pyproject.toml b/...tationPipeline/ManualQCPRS/pyproject.toml → PRS/ManualQCPRS/pyproject.toml
diff --git a/...ine/ManualQCPRS/tests/ManualQCPRSTests.py → PRS/ManualQCPRS/tests/ManualQCPRSTests.py b/...ine/ManualQCPRS/tests/ManualQCPRSTests.py → PRS/ManualQCPRS/tests/ManualQCPRSTests.py
diff --git a/...ualQCPRS/tests/resources/test_results.tsv → ...ualQCPRS/tests/resources/test_results.tsv b/...ualQCPRS/tests/resources/test_results.tsv → ...ualQCPRS/tests/resources/test_results.tsv
diff --git a/...lQCPRS/tests/resources/test_results_2.tsv → ...lQCPRS/tests/resources/test_results_2.tsv b/...lQCPRS/tests/resources/test_results_2.tsv → ...lQCPRS/tests/resources/test_results_2.tsv
diff --git a/...lQCPRS/tests/resources/test_results_3.tsv → ...lQCPRS/tests/resources/test_results_3.tsv b/...lQCPRS/tests/resources/test_results_3.tsv → ...lQCPRS/tests/resources/test_results_3.tsv
diff --git a/ImputationPipeline/PCARE.wdl → PRS/PCARE.wdl b/ImputationPipeline/PCARE.wdl → PRS/PCARE.wdl
diff --git a/ImputationPipeline/PCAREAndQC.wdl → PRS/PCAREAndQC.wdl b/ImputationPipeline/PCAREAndQC.wdl → PRS/PCAREAndQC.wdl
diff --git a/ImputationPipeline/PCATasks.wdl → PRS/PCATasks.wdl b/ImputationPipeline/PCATasks.wdl → PRS/PCATasks.wdl
diff --git a/ImputationPipeline/PRSWrapper.wdl → PRS/PRSWrapper.wdl b/ImputationPipeline/PRSWrapper.wdl → PRS/PRSWrapper.wdl
diff --git a/ImputationPipeline/PerformPopulationPCA.wdl → PRS/PerformPopulationPCA.wdl b/ImputationPipeline/PerformPopulationPCA.wdl → PRS/PerformPopulationPCA.wdl
diff --git a/ImputationPipeline/ScoreBGE/Dockerfile → PRS/ScoreBGE/Dockerfile b/ImputationPipeline/ScoreBGE/Dockerfile → PRS/ScoreBGE/Dockerfile
diff --git a/ImputationPipeline/ScoreBGE/ScoreBGE.py → PRS/ScoreBGE/ScoreBGE.py b/ImputationPipeline/ScoreBGE/ScoreBGE.py → PRS/ScoreBGE/ScoreBGE.py
diff --git a/ImputationPipeline/ScoreBGE/ScoreBGE.wdl → PRS/ScoreBGE/ScoreBGE.wdl b/ImputationPipeline/ScoreBGE/ScoreBGE.wdl → PRS/ScoreBGE/ScoreBGE.wdl
diff --git a/...tationPipeline/ScoreBGE/tests/__init__.py → PRS/ScoreBGE/tests/__init__.py b/...tationPipeline/ScoreBGE/tests/__init__.py → PRS/ScoreBGE/tests/__init__.py
diff --git a/...output.any_source_any_sample.sites_scored → ...output.any_source_any_sample.sites_scored b/...output.any_source_any_sample.sites_scored → ...output.any_source_any_sample.sites_scored
diff --git a/...d_output/expected_output.exome_gvcf.score → ...d_output/expected_output.exome_gvcf.score b/...d_output/expected_output.exome_gvcf.score → ...d_output/expected_output.exome_gvcf.score
diff --git a/...t/expected_output.exome_gvcf.sites_scored → ...t/expected_output.exome_gvcf.sites_scored b/...t/expected_output.exome_gvcf.sites_scored → ...t/expected_output.exome_gvcf.sites_scored
diff --git a/...put/expected_output.imputed_wgs_vcf.score → ...put/expected_output.imputed_wgs_vcf.score b/...put/expected_output.imputed_wgs_vcf.score → ...put/expected_output.imputed_wgs_vcf.score
diff --git a/...ected_output.imputed_wgs_vcf.sites_scored → ...ected_output.imputed_wgs_vcf.sites_scored b/...ected_output.imputed_wgs_vcf.sites_scored → ...ected_output.imputed_wgs_vcf.sites_scored
diff --git a/...ned/expected_output/expected_output.score → ...ned/expected_output/expected_output.score b/...ned/expected_output/expected_output.score → ...ned/expected_output/expected_output.score
diff --git a/...resources/combined/test_combined.wes.gvcf → ...resources/combined/test_combined.wes.gvcf b/...resources/combined/test_combined.wes.gvcf → ...resources/combined/test_combined.wes.gvcf
diff --git a/...ources/combined/test_combined.wes.gvcf.gz → ...ources/combined/test_combined.wes.gvcf.gz b/...ources/combined/test_combined.wes.gvcf.gz → ...ources/combined/test_combined.wes.gvcf.gz
diff --git a/...es/combined/test_combined.wes.gvcf.gz.tbi → ...es/combined/test_combined.wes.gvcf.gz.tbi b/...es/combined/test_combined.wes.gvcf.gz.tbi → ...es/combined/test_combined.wes.gvcf.gz.tbi
diff --git a/.../resources/combined/test_combined.wgs.vcf → .../resources/combined/test_combined.wgs.vcf b/.../resources/combined/test_combined.wgs.vcf → .../resources/combined/test_combined.wgs.vcf
diff --git a/...sources/combined/test_combined.wgs.vcf.gz → ...sources/combined/test_combined.wgs.vcf.gz b/...sources/combined/test_combined.wgs.vcf.gz → ...sources/combined/test_combined.wgs.vcf.gz
diff --git a/...ces/combined/test_combined.wgs.vcf.gz.tbi → ...ces/combined/test_combined.wgs.vcf.gz.tbi b/...ces/combined/test_combined.wgs.vcf.gz.tbi → ...ces/combined/test_combined.wgs.vcf.gz.tbi
diff --git a/...ources/combined/test_weights_combined.txt → ...ources/combined/test_weights_combined.txt b/...ources/combined/test_weights_combined.txt → ...ources/combined/test_weights_combined.txt
diff --git a/...ipeline/ScoreBGE/tests/resources/ref.dict → PRS/ScoreBGE/tests/resources/ref.dict b/...ipeline/ScoreBGE/tests/resources/ref.dict → PRS/ScoreBGE/tests/resources/ref.dict
diff --git a/...BGE/tests/resources/test_weights_read.txt → ...BGE/tests/resources/test_weights_read.txt b/...BGE/tests/resources/test_weights_read.txt → ...BGE/tests/resources/test_weights_read.txt
diff --git a/.../wes_gvcf_ref_blocks/test_ref_blocks.gvcf → .../wes_gvcf_ref_blocks/test_ref_blocks.gvcf b/.../wes_gvcf_ref_blocks/test_ref_blocks.gvcf → .../wes_gvcf_ref_blocks/test_ref_blocks.gvcf
diff --git a/...s_gvcf_ref_blocks/test_ref_blocks.gvcf.gz → ...s_gvcf_ref_blocks/test_ref_blocks.gvcf.gz b/...s_gvcf_ref_blocks/test_ref_blocks.gvcf.gz → ...s_gvcf_ref_blocks/test_ref_blocks.gvcf.gz
diff --git a/...cf_ref_blocks/test_ref_blocks.gvcf.gz.tbi → ...cf_ref_blocks/test_ref_blocks.gvcf.gz.tbi b/...cf_ref_blocks/test_ref_blocks.gvcf.gz.tbi → ...cf_ref_blocks/test_ref_blocks.gvcf.gz.tbi
diff --git a/...cf_ref_blocks/test_weights_ref_blocks.txt → ...cf_ref_blocks/test_weights_ref_blocks.txt b/...cf_ref_blocks/test_weights_ref_blocks.txt → ...cf_ref_blocks/test_weights_ref_blocks.txt
diff --git a/...wes_gvcf_variants/test_gvcf_variants.gvcf → ...wes_gvcf_variants/test_gvcf_variants.gvcf b/...wes_gvcf_variants/test_gvcf_variants.gvcf → ...wes_gvcf_variants/test_gvcf_variants.gvcf
diff --git a/..._gvcf_variants/test_gvcf_variants.gvcf.gz → ..._gvcf_variants/test_gvcf_variants.gvcf.gz b/..._gvcf_variants/test_gvcf_variants.gvcf.gz → ..._gvcf_variants/test_gvcf_variants.gvcf.gz
diff --git a/...f_variants/test_gvcf_variants.gvcf.gz.tbi → ...f_variants/test_gvcf_variants.gvcf.gz.tbi b/...f_variants/test_gvcf_variants.gvcf.gz.tbi → ...f_variants/test_gvcf_variants.gvcf.gz.tbi
diff --git a/...f_variants/test_weights_gvcf_variants.txt → ...f_variants/test_weights_gvcf_variants.txt b/...f_variants/test_weights_gvcf_variants.txt → ...f_variants/test_weights_gvcf_variants.txt
diff --git a/...esources/wgs_vcf/test_weights_wgs_vcf.txt → ...esources/wgs_vcf/test_weights_wgs_vcf.txt b/...esources/wgs_vcf/test_weights_wgs_vcf.txt → ...esources/wgs_vcf/test_weights_wgs_vcf.txt
diff --git a/...eBGE/tests/resources/wgs_vcf/test_wgs.vcf → ...eBGE/tests/resources/wgs_vcf/test_wgs.vcf b/...eBGE/tests/resources/wgs_vcf/test_wgs.vcf → ...eBGE/tests/resources/wgs_vcf/test_wgs.vcf
diff --git a/...E/tests/resources/wgs_vcf/test_wgs.vcf.gz → ...E/tests/resources/wgs_vcf/test_wgs.vcf.gz b/...E/tests/resources/wgs_vcf/test_wgs.vcf.gz → ...E/tests/resources/wgs_vcf/test_wgs.vcf.gz
diff --git a/...sts/resources/wgs_vcf/test_wgs.vcf.gz.tbi → ...sts/resources/wgs_vcf/test_wgs.vcf.gz.tbi b/...sts/resources/wgs_vcf/test_wgs.vcf.gz.tbi → ...sts/resources/wgs_vcf/test_wgs.vcf.gz.tbi
diff --git a/...nPipeline/ScoreBGE/tests/test_ScoreBGE.py → PRS/ScoreBGE/tests/test_ScoreBGE.py b/...nPipeline/ScoreBGE/tests/test_ScoreBGE.py → PRS/ScoreBGE/tests/test_ScoreBGE.py
diff --git a/ImputationPipeline/ScoringPart.wdl → PRS/ScoringPart.wdl b/ImputationPipeline/ScoringPart.wdl → PRS/ScoringPart.wdl
diff --git a/ImputationPipeline/ScoringTasks.wdl → PRS/ScoringTasks.wdl b/ImputationPipeline/ScoringTasks.wdl → PRS/ScoringTasks.wdl
diff --git a/ImputationPipeline/Structs.wdl → PRS/Structs.wdl b/ImputationPipeline/Structs.wdl → PRS/Structs.wdl
diff --git a/...Pipeline/TrainAncestryAdjustmentModel.wdl → PRS/TrainAncestryAdjustmentModel.wdl b/...Pipeline/TrainAncestryAdjustmentModel.wdl → PRS/TrainAncestryAdjustmentModel.wdl
diff --git a/...onPipeline/Validation/SubsetWeightSet.wdl → PRS/Validation/SubsetWeightSet.wdl b/...onPipeline/Validation/SubsetWeightSet.wdl → PRS/Validation/SubsetWeightSet.wdl
diff --git a/...onPipeline/Validation/ValidateScoring.wdl → PRS/Validation/ValidateScoring.wdl b/...onPipeline/Validation/ValidateScoring.wdl → PRS/Validation/ValidateScoring.wdl
diff --git a/ImputationPipeline/__init__.py → PRS/__init__.py b/ImputationPipeline/__init__.py → PRS/__init__.py
diff --git a/ImputationPipeline/build_push_docker.sh → PRS/build_push_docker.sh b/ImputationPipeline/build_push_docker.sh → PRS/build_push_docker.sh
diff --git a/...tationPipeline/flashpca_docker/Dockerfile → PRS/flashpca_docker/Dockerfile b/...tationPipeline/flashpca_docker/Dockerfile → PRS/flashpca_docker/Dockerfile
diff --git a/...ation_bcftools_vcftools_docker/Dockerfile → ...ation_bcftools_vcftools_docker/Dockerfile b/...ation_bcftools_vcftools_docker/Dockerfile → ...ation_bcftools_vcftools_docker/Dockerfile
diff --git a/...ker/build_push_vcftoolsbcftools_docker.sh → ...ker/build_push_vcftoolsbcftools_docker.sh b/...ker/build_push_vcftoolsbcftools_docker.sh → ...ker/build_push_vcftoolsbcftools_docker.sh
diff --git a/...peline/imputation_eagle_docker/Dockerfile → PRS/imputation_eagle_docker/Dockerfile b/...peline/imputation_eagle_docker/Dockerfile → PRS/imputation_eagle_docker/Dockerfile
diff --git a/...n_eagle_docker/build_push_eagle_docker.sh → ...n_eagle_docker/build_push_eagle_docker.sh b/...n_eagle_docker/build_push_eagle_docker.sh → ...n_eagle_docker/build_push_eagle_docker.sh
diff --git a/.../imputation_interaction_python/Dockerfile → PRS/imputation_interaction_python/Dockerfile b/.../imputation_interaction_python/Dockerfile → PRS/imputation_interaction_python/Dockerfile
diff --git a/ImputationPipeline/plink2_docker/Dockerfile → PRS/plink2_docker/Dockerfile b/ImputationPipeline/plink2_docker/Dockerfile → PRS/plink2_docker/Dockerfile
diff --git a/...ne/tidyverse_kableextra_docker/Dockerfile → PRS/tidyverse_kableextra_docker/Dockerfile b/...ne/tidyverse_kableextra_docker/Dockerfile → PRS/tidyverse_kableextra_docker/Dockerfile
diff --git a/..._docker/build_push_r_kableextra_docker.sh → ..._docker/build_push_r_kableextra_docker.sh b/..._docker/build_push_r_kableextra_docker.sh → ..._docker/build_push_r_kableextra_docker.sh