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.gitignore
.markdownlint.json
.pre-commit-config.yaml
.python-version
CHANGELOG.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
Dockerfile
LICENSE
Makefile
README.md
WORKFLOWS.md
pyproject.toml
sonar-project.properties
uv.lock
.github/renovate-config.json
.github/workflows/docker.yaml
.github/workflows/lint.yaml
.github/workflows/package.yaml
.github/workflows/renovate.yaml
.github/workflows/security.yaml
.github/workflows/test.yaml
.github/workflows/web-docs.yaml
assets/DNA_CURIOUS_FLOYD_CROPPED.png
assets/KEYBOARD_HAPPY_FLOYD.png
assets/newplot.png
docs/badges.yaml
docs/mkdocs.yml
docs/workflow_descriptions.yaml
docs/docs/changelog.md
docs/docs/code-analysis-consistency.
docs/docs/code-analysis-consistency.md
docs/docs/considerations-limitations.md
docs/docs/docker.md
docs/docs/index.md
docs/docs/installation.md
docs/docs/tests.md
docs/docs/usage.md
docs/docs/workflows.md
docs/docs/assets/DNA_CURIOUS_FLOYD_CROPPED.png
docs/docs/assets/KEYBOARD_HAPPY_FLOYD.png
docs/docs/assets/favicon.png
docs/docs/assets/logo-colour.svg
docs/docs/assets/newplot.png
docs/docs/reference/filetypes.md
docs/docs/reference/index.md
docs/docs/reference/inputs.md
docs/docs/reference/metamist.md
docs/docs/reference/pedigree_info.md
docs/docs/reference/resources.md
docs/docs/reference/stage.md
docs/docs/reference/status.md
docs/docs/reference/targets.md
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src/__init__.py
src/cpg_flow/__init__.py
src/cpg_flow/defaults.toml
src/cpg_flow/filetypes.py
src/cpg_flow/inputs.py
src/cpg_flow/metamist.py
src/cpg_flow/resources.py
src/cpg_flow/stage.py
src/cpg_flow/status.py
src/cpg_flow/utils.py
src/cpg_flow/workflow.py
src/cpg_flow.egg-info/PKG-INFO
src/cpg_flow.egg-info/SOURCES.txt
src/cpg_flow.egg-info/dependency_links.txt
src/cpg_flow.egg-info/requires.txt
src/cpg_flow.egg-info/top_level.txt
src/cpg_flow/show_workflow/graph.py
src/cpg_flow/targets/__init__.py
src/cpg_flow/targets/cohort.py
src/cpg_flow/targets/dataset.py
src/cpg_flow/targets/helpers.py
src/cpg_flow/targets/multicohort.py
src/cpg_flow/targets/pedigree_info.py
src/cpg_flow/targets/sequencing_group.py
src/cpg_flow/targets/target.py
src/cpg_flow/targets/types.py
tests/README.md
tests/__init__.py
tests/conftest.py
tests/test_cohort.py
tests/test_metamist.py
tests/test_multicohort.py
tests/test_status.py
tests/test_workflow.py
tests/assets/test_cohort/COH1.json
tests/assets/test_cohort/COH2.json
tests/assets/test_cohort/COH3.json
tests/assets/test_cohort/COH4.json
tests/assets/test_cohort/COH5.json
tests/assets/test_cohort/pedigree.json
tests/assets/test_multicohort/COH1.json
tests/assets/test_multicohort/COH123.json
tests/assets/test_multicohort/COH2.json
tests/assets/test_multicohort/COH456.json
tests/assets/test_multicohort/pedigree.json
tests/stages/__init__.py
tests/stages/test_first_last_stages.py
tests/stages/test_first_last_stages_misconfigured.py
tests/stages/test_force_stages.py
tests/stages/test_last_stages.py
tests/stages/test_only_stages.py
tests/stages/test_skip_stages.py
tests/stages/test_skip_stages_fail.py
tests/stages/test_stage_types.py