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pyproject.toml
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[tool.poetry]
name = "cgr_gwas_qc"
version = "1.8.0-rc2"
description = "The CGR GWAS QC Pipeline"
authors = [
"Justin Fear <justin.fear@nih.gov>",
"Jiahui Wang <jiahui.wang2@nih.gov>",
"Jai Liu <jia.liu3@nih.gov>",
"Eric Karlins",
"Bari Ballew <bari.ballew@nih.gov>",
"Cameron Palmer <cameron.palmer@nih.gov>",
"Bin Zhu <bin.zhu2@nih.gov>",
"Kevin Liao <kliao@rti.org>",
"Caryn Willis <cdwillis@rti.org>",
"Jesse Marks <jmarks@rti.org>"
]
readme = "README.md"
repository = "https://github.com/NCI-CGR/GwasQcPipeline.git"
keywords = ["GWAS", "cancer", "QC", "snakemake"]
packages = [
{ include = "cgr_gwas_qc", from = "src"}
]
[tool.poetry.dependencies]
python = "^3.8.1"
typer = "^0.12.5"
pandas = "^2.0.3"
snakemake = "^6.0.0"
pysam = "^0.21.0"
ryd = "^0.7.1"
pydantic = "^1.0.0"
networkx = "^3.1"
Jinja2 = ">=2.3, <3.0"
more-itertools = "^10.1.0"
seaborn = "^0.12.2"
python-ternary = "^1.0.8"
tabulate = "^0.8.0"
openpyxl = "^3.1.2"
markupsafe = "~2.0"
pulp = "2.7.0"
[tool.poetry.dev-dependencies]
black = { version = "24.8.0" }
flake8 = { version = "^5.0.0", python = ">=3.8,<4.0"}
snakefmt = "^0.10.2"
importlib-metadata = "^8.5.0"
pytest = "^7.4.1"
mypy = "^1.5.1"
isort = "^5.12.0"
pre-commit = "^3.4.0"
rstcheck = "^5.0.0"
ipykernel = "^6.25.2"
pytest-xdist = "^3.3.1"
commitizen = "^2.0.0"
ptvsd = "^4.3.2"
rope = "^1.9.0"
pytest-mock = "^3.11.1"
Pillow = "^10.0.0"
sphinx = "3.2.1"
sphinxcontrib-mermaid = "0.4.0"
sphinx-rtd-theme = "0.5.0"
sphinx-prompt = "*"
sphinx-pydantic = "0.1.1"
sphinx-jsonschema = "1.15"
Sphinx-Substitution-Extensions = "2020.9.30"
sphinx-click = "3.0.1"
[tool.poetry.scripts]
cgr = "cgr_gwas_qc.cli:app"
legacy_compare = "cgr_gwas_qc.scripts.legacy_compare:app"
[tool.isort]
profile = "black"
line_length = 100
[tool.black]
line-length = 100
[tool.pytest.ini_options]
markers = [
"regression: Functional tests to compare with outputs from legacy workflow.",
"workflow: Snakemake workflow tests, partial integration tests for snakemake modules.",
"real_data: Mark test to run if we can use real internal data.",
"slow: Marks tests that take a really long time to run."
]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"