LICENSE
README.md
pyproject.toml
setup.py
cpg_workflows/__init__.py
cpg_workflows/batch.py
cpg_workflows/filetypes.py
cpg_workflows/inputs.py
cpg_workflows/metamist.py
cpg_workflows/resources.py
cpg_workflows/slack.py
cpg_workflows/status.py
cpg_workflows/targets.py
cpg_workflows/utils.py
cpg_workflows/workflow.py
cpg_workflows.egg-info/PKG-INFO
cpg_workflows.egg-info/SOURCES.txt
cpg_workflows.egg-info/dependency_links.txt
cpg_workflows.egg-info/requires.txt
cpg_workflows.egg-info/top_level.txt
cpg_workflows/jobs/__init__.py
cpg_workflows/jobs/align.py
cpg_workflows/jobs/fastqc.py
cpg_workflows/jobs/genotype.py
cpg_workflows/jobs/happy.py
cpg_workflows/jobs/joint_genotyping.py
cpg_workflows/jobs/multiqc.py
cpg_workflows/jobs/picard.py
cpg_workflows/jobs/samtools.py
cpg_workflows/jobs/seqr_loader.py
cpg_workflows/jobs/somalier.py
cpg_workflows/jobs/vcf.py
cpg_workflows/jobs/vep.py
cpg_workflows/jobs/verifybamid.py
cpg_workflows/jobs/vqsr.py
cpg_workflows/large_cohort/__init__.py
cpg_workflows/large_cohort/ancestry_pca.py
cpg_workflows/large_cohort/ancestry_plots.py
cpg_workflows/large_cohort/combiner.py
cpg_workflows/large_cohort/dataproc_script.py
cpg_workflows/large_cohort/dataproc_utils.py
cpg_workflows/large_cohort/dense_subset.py
cpg_workflows/large_cohort/frequencies.py
cpg_workflows/large_cohort/load_vqsr.py
cpg_workflows/large_cohort/relatedness.py
cpg_workflows/large_cohort/sample_qc.py
cpg_workflows/large_cohort/site_only_vcf.py
cpg_workflows/python_scripts/__init__.py
cpg_workflows/python_scripts/check_multiqc.py
cpg_workflows/python_scripts/check_pedigree.py
cpg_workflows/query_modules/__init__.py
cpg_workflows/query_modules/seqr_loader.py
cpg_workflows/query_modules/vep.py
cpg_workflows/stages/__init__.py
cpg_workflows/stages/align.py
cpg_workflows/stages/cram_qc.py
cpg_workflows/stages/fastqc.py
cpg_workflows/stages/gatk_sv.py
cpg_workflows/stages/genotype.py
cpg_workflows/stages/gvcf_qc.py
cpg_workflows/stages/joint_genotyping.py
cpg_workflows/stages/joint_genotyping_qc.py
cpg_workflows/stages/large_cohort.py
cpg_workflows/stages/seqr_loader.py
cpg_workflows/stages/vep.py
cpg_workflows/stages/vqsr.py
seqr-loading-pipelines/__init__.py
seqr-loading-pipelines/gcloud_dataproc/__init__.py
seqr-loading-pipelines/gcloud_dataproc/create_es_loading_nodes.py
seqr-loading-pipelines/gcloud_dataproc/create_persistent_es_nodes.py
seqr-loading-pipelines/gcloud_dataproc/submit.py
seqr-loading-pipelines/gcloud_dataproc/utils/__init__.py
seqr-loading-pipelines/gcloud_dataproc/utils/machine_types.py
seqr-loading-pipelines/gcloud_dataproc/v02/__init__.py
seqr-loading-pipelines/gcloud_dataproc/v02/create_cluster_without_VEP.py
seqr-loading-pipelines/gcloud_dataproc/v02/run_script.py
seqr-loading-pipelines/hail_scripts/__init__.py
seqr-loading-pipelines/hail_scripts/computed_fields/__init__.py
seqr-loading-pipelines/hail_scripts/computed_fields/flags.py
seqr-loading-pipelines/hail_scripts/computed_fields/test_flags.py
seqr-loading-pipelines/hail_scripts/computed_fields/test_variant_id.py
seqr-loading-pipelines/hail_scripts/computed_fields/variant_id.py
seqr-loading-pipelines/hail_scripts/computed_fields/vep.py
seqr-loading-pipelines/hail_scripts/elasticsearch/__init__.py
seqr-loading-pipelines/hail_scripts/elasticsearch/elasticsearch_client_v7.py
seqr-loading-pipelines/hail_scripts/elasticsearch/elasticsearch_utils.py
seqr-loading-pipelines/hail_scripts/elasticsearch/elasticsearch_utils_tests.py
seqr-loading-pipelines/hail_scripts/elasticsearch/hail_elasticsearch_client.py
seqr-loading-pipelines/hail_scripts/update_models/__init__.py
seqr-loading-pipelines/hail_scripts/update_models/update_mt_schema.py
seqr-loading-pipelines/hail_scripts/utils/__init__.py
seqr-loading-pipelines/hail_scripts/utils/clinvar.py
seqr-loading-pipelines/hail_scripts/utils/hail_utils.py
seqr-loading-pipelines/kubernetes/__init__.py
seqr-loading-pipelines/kubernetes/kubectl_utils.py
seqr-loading-pipelines/kubernetes/network_utils.py
seqr-loading-pipelines/kubernetes/shell_utils.py
seqr-loading-pipelines/kubernetes/yaml_settings_utils.py
seqr-loading-pipelines/sv_pipeline/__init__.py
seqr-loading-pipelines/sv_pipeline/exome/__init__.py
seqr-loading-pipelines/sv_pipeline/exome/load_data.py
seqr-loading-pipelines/sv_pipeline/genome/__init__.py
seqr-loading-pipelines/sv_pipeline/genome/load_data.py
seqr-loading-pipelines/sv_pipeline/genome/load_data_tests.py
seqr-loading-pipelines/sv_pipeline/genome/run_dataproc_load_data.py
seqr-loading-pipelines/sv_pipeline/genome/utils/__init__.py
seqr-loading-pipelines/sv_pipeline/genome/utils/download_utils.py
seqr-loading-pipelines/sv_pipeline/genome/utils/download_utils_tests.py
seqr-loading-pipelines/sv_pipeline/genome/utils/mapping_gene_ids.py
seqr-loading-pipelines/sv_pipeline/genome/utils/mapping_gene_ids_tests.py
seqr-loading-pipelines/sv_pipeline/utils/__init__.py
seqr-loading-pipelines/sv_pipeline/utils/common.py
test/test_batch.py
test/test_check_multiqc.py
test/test_check_pedigree.py
test/test_cohort.py
test/test_large_cohort.py
test/test_seqr_loader_dry.py
test/test_status.py
test/test_workflow.py