LICENSE
MANIFEST.in
README.md
setup.py
hifi_solves_run_humanwgs/__init__.py
hifi_solves_run_humanwgs/constants.py
hifi_solves_run_humanwgs/logger.py
hifi_solves_run_humanwgs/upload_and_run.py
hifi_solves_run_humanwgs/workbench.py
hifi_solves_run_humanwgs.egg-info/PKG-INFO
hifi_solves_run_humanwgs.egg-info/SOURCES.txt
hifi_solves_run_humanwgs.egg-info/dependency_links.txt
hifi_solves_run_humanwgs.egg-info/entry_points.txt
hifi_solves_run_humanwgs.egg-info/requires.txt
hifi_solves_run_humanwgs.egg-info/top_level.txt
hifi_solves_run_humanwgs/__pycache__/__init__.cpython-313.pyc
hifi_solves_run_humanwgs/__pycache__/constants.cpython-313.pyc
hifi_solves_run_humanwgs/__pycache__/logger.cpython-313.pyc
hifi_solves_run_humanwgs/__pycache__/upload_and_run.cpython-313.pyc
hifi_solves_run_humanwgs/__pycache__/workbench.cpython-313.pyc
hifi_solves_run_humanwgs/backends/__init__.py
hifi_solves_run_humanwgs/backends/aws.py
hifi_solves_run_humanwgs/backends/azure.py
hifi_solves_run_humanwgs/backends/gcp.py
hifi_solves_run_humanwgs/backends/parameter_override.py
hifi_solves_run_humanwgs/backends/__pycache__/__init__.cpython-313.pyc
hifi_solves_run_humanwgs/backends/__pycache__/aws.cpython-313.pyc
hifi_solves_run_humanwgs/backends/__pycache__/azure.cpython-313.pyc
hifi_solves_run_humanwgs/backends/__pycache__/gcp.cpython-313.pyc
hifi_solves_run_humanwgs/backends/__pycache__/parameter_override.cpython-313.pyc
hifi_solves_run_humanwgs/instruments/dnastack.sample-sync.json
hifi_solves_run_humanwgs/instruments/transformation.js
hifi_solves_run_humanwgs/workflows/__init__.py
hifi_solves_run_humanwgs/workflows/hifisolves_wrapper.wdl
hifi_solves_run_humanwgs/workflows/input_template.aws-healthomics.json
hifi_solves_run_humanwgs/workflows/input_template.azure.json
hifi_solves_run_humanwgs/workflows/input_template.gcp.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.dockstore.yml
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.git
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.gitignore
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.gitmodules
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/GRCh38.ref_map.v2p0p0.template.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/GRCh38.tertiary_map.v2p0p0.template.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/LICENSE
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/README.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/image_manifest.txt
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/wdl-ci.config.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.claude/settings.local.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.github/ISSUE_TEMPLATE/bug_report.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.github/ISSUE_TEMPLATE/feature_request.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/.github/workflows/lint-test-workflows.yml
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/aws-healthomics/GRCh38.ref_map.v2p0p0.aws.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/aws-healthomics/GRCh38.tertiary_map.v2p0p0.aws.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/aws-healthomics/aws_ecr_push_tag_images.sh
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/aws-healthomics/family.healthomics.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/aws-healthomics/singleton.healthomics.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/azure/GRCh38.ref_map.v2p0p0.azure.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/azure/GRCh38.tertiary_map.v2p0p0.azure.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/azure/family.azure.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/azure/singleton.azure.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/gcp/GRCh38.ref_map.v2p0p0.gcp.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/gcp/GRCh38.tertiary_map.v2p0p0.gcp.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/gcp/family.gcp.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/gcp/singleton.gcp.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/hpc/GRCh38.ref_map.v2p0p0.hpc.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/hpc/GRCh38.tertiary_map.v2p0p0.hpc.tsv
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/hpc/family.hpc.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/hpc/miniwdl.cfg
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/backends/hpc/singleton.hpc.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backend-aws-healthomics.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backend-azure.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backend-dnanexus.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backend-gcp.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backend-hpc.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/backends.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/bam_stats.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/deepvariant.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/family.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/gpu.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/pharmcat.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/ref_map.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/singleton.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/tertiary.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/tertiary_map.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/docs/tools_containers.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/images/logo_wdl_workflows.svg
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/scripts/create_image_manifest.sh
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/scripts/update_docs.sh
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/family.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/family.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/humanwgs_structs.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/singleton.inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/singleton.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/downstream/downstream.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/downstream/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/joint/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/joint/joint.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/tertiary/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/tertiary/tertiary.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/upstream/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/upstream/upstream.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/.git
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/LICENSE
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/README.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/.github/pull_request_template.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/Dockerfile
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/build.env
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/detect_duplicate_rgs/.gitignore
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/detect_duplicate_rgs/setup.py
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/detect_duplicate_rgs/detect_duplicate_rgs/__init__.py
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/detect_duplicate_rgs/detect_duplicate_rgs/detect_duplicate_rgs.py
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/docker/pbmm2_jasmine/detect_duplicate_rgs/tests/test_detect.py
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/images/logo_wdl_workflows.svg
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/structs.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/bcftools.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/cpg_pileup.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/glnexus.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/hificnv.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/hiphase.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/merge_bam_stats.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/mosdepth.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/paraphase.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/pbmm2.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/pbstarphase.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/pbsv.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/samtools.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/trgt.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/utilities.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/tasks/write_ped_phrank.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/backend_configuration/backend_configuration.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/deepvariant/README.md
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/deepvariant/deepvariant.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/deepvariant/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/get_pbsv_splits/get_pbsv_splits.wdl
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/get_pbsv_splits/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/pharmcat/inputs.json
hifi_solves_run_humanwgs/workflows/HiFi-human-WGS-WDL/workflows/wdl-common/wdl/workflows/pharmcat/pharmcat.wdl
hifi_solves_run_humanwgs/workflows/__pycache__/__init__.cpython-313.pyc
tests/__init__.py
tests/test_aws.py
tests/test_azure.py
tests/test_gcp.py
tests/test_generate_inputs.py
tests/test_upload_and_run.py
tests/test_workbench.py