LICENSE
README.md
pyproject.toml
setup.py
cpg_workflows/__init__.py
cpg_workflows/batch.py
cpg_workflows/defaults.toml
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/dataproc_scripts/__init__.py
cpg_workflows/dataproc_scripts/annotate_cohort.py
cpg_workflows/dataproc_scripts/annotate_dataset.py
cpg_workflows/dataproc_scripts/mt_to_es.py
cpg_workflows/dataproc_scripts/vep_json_to_ht.py
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/stripy.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/stripy.py
cpg_workflows/stages/vep.py
cpg_workflows/stages/vqsr.py
test/__init__.py
test/conftest.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
test/stages/__init__.py
test/stages/test_first_last_stages.py
test/stages/test_first_last_stages_misconfigured.py
test/stages/test_first_stages.py
test/stages/test_force_stages.py
test/stages/test_last_stages.py
test/stages/test_skip_stages.py
test/stages/test_skip_stages_fail.py