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/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/entry_points.txt
cpg_workflows.egg-info/requires.txt
cpg_workflows.egg-info/top_level.txt
cpg_workflows/dataproc_scripts/__init__.py
cpg_workflows/dataproc_scripts/mt_to_es.py
cpg_workflows/dataproc_scripts/pca_runner.py
cpg_workflows/jobs/__init__.py
cpg_workflows/jobs/align.py
cpg_workflows/jobs/align_rna.py
cpg_workflows/jobs/bam_to_cram.py
cpg_workflows/jobs/bcftools.py
cpg_workflows/jobs/count.py
cpg_workflows/jobs/exomiser.py
cpg_workflows/jobs/fastqc.py
cpg_workflows/jobs/fraser.py
cpg_workflows/jobs/gatk_sv.py
cpg_workflows/jobs/gcnv.py
cpg_workflows/jobs/genotype.py
cpg_workflows/jobs/happy.py
cpg_workflows/jobs/joint_genotyping.py
cpg_workflows/jobs/markdups.py
cpg_workflows/jobs/mito.py
cpg_workflows/jobs/multiqc.py
cpg_workflows/jobs/outrider.py
cpg_workflows/jobs/picard.py
cpg_workflows/jobs/ploidy_table_from_ped.py
cpg_workflows/jobs/sample_batching.py
cpg_workflows/jobs/samtools.py
cpg_workflows/jobs/seqr_loader.py
cpg_workflows/jobs/seqr_loader_sv.py
cpg_workflows/jobs/simple_vep_annotation.py
cpg_workflows/jobs/somalier.py
cpg_workflows/jobs/stripy.py
cpg_workflows/jobs/trim.py
cpg_workflows/jobs/validation.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/seqr_loader_cnv.py
cpg_workflows/query_modules/seqr_loader_sv.py
cpg_workflows/query_modules/validation.py
cpg_workflows/query_modules/vep.py
cpg_workflows/scripts/__init__.py
cpg_workflows/scripts/collect_dataset_tsvs.py
cpg_workflows/scripts/extract_vcf_from_mt.py
cpg_workflows/scripts/generate_intervals_wrapper.py
cpg_workflows/scripts/generate_new_intervals.py
cpg_workflows/scripts/gvcfs_to_vcf.py
cpg_workflows/scripts/long_read_sniffles_vcf_modifier.py
cpg_workflows/scripts/mt_from_vds.py
cpg_workflows/scripts/mt_to_es_without_dataproc.py
cpg_workflows/scripts/upgrade_ped_with_inferred.py
cpg_workflows/scripts/vds_from_gvcfs.py
cpg_workflows/stages/__init__.py
cpg_workflows/stages/align.py
cpg_workflows/stages/clinvarbitration.py
cpg_workflows/stages/count.py
cpg_workflows/stages/cram_qc.py
cpg_workflows/stages/exomiser.py
cpg_workflows/stages/fastqc.py
cpg_workflows/stages/fraser.py
cpg_workflows/stages/gcnv.py
cpg_workflows/stages/genotype.py
cpg_workflows/stages/gvcf_qc.py
cpg_workflows/stages/happy_validation.py
cpg_workflows/stages/joint_genotyping.py
cpg_workflows/stages/joint_genotyping_qc.py
cpg_workflows/stages/large_cohort.py
cpg_workflows/stages/mito.py
cpg_workflows/stages/outrider.py
cpg_workflows/stages/seqr_loader.py
cpg_workflows/stages/stripy.py
cpg_workflows/stages/talos.py
cpg_workflows/stages/trim_align.py
cpg_workflows/stages/vep.py
cpg_workflows/stages/vqsr.py
cpg_workflows/stages/gatk_sv/__init__.py
cpg_workflows/stages/gatk_sv/gatk_sv_common.py
cpg_workflows/stages/gatk_sv/gatk_sv_multisample.py
cpg_workflows/stages/gatk_sv/gatk_sv_single_sample.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_gatk_sv_methods.py
test/test_large_cohort.py
test/test_lr_sv_mods.py
test/test_metamist.py
test/test_multicohort.py
test/test_seqr_loader_dry.py
test/test_size.py
test/test_status.py
test/test_workflow.py
test/factories/__init__.py
test/factories/alignment_input.py
test/factories/batch.py
test/factories/config.py
test/factories/dataset.py
test/factories/sequencing_group.py
test/factories/types.py
test/jobs/__init__.py
test/jobs/helpers.py
test/jobs/test_fastqc.py
test/jobs/test_gatk_sv.py
test/jobs/test_picard.py
test/jobs/test_samtools.py
test/jobs/test_verifybamid.py
test/jobs/somalier/__init__.py
test/jobs/somalier/test_check_pedigree.py
test/jobs/somalier/test_extract.py
test/jobs/somalier/test_relate.py
test/jobs/test_align/__init__.py
test/jobs/test_align/shared.py
test/jobs/test_align/test_bam_cram.py
test/jobs/test_align/test_biobambam.py
test/jobs/test_align/test_fastq.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_only_stages.py
test/stages/test_skip_stages.py
test/stages/test_skip_stages_fail.py
test/stages/test_stage_types.py