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            "Environment :: Plugins",
            "Framework :: Pytest",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
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        "description": "[![Travis CI](https://travis-ci.com/EliLillyCo/pytest-wdl.svg?branch=master)](https://travis-ci.com/EliLillyCo/pytest-wdl)\n[![Code Coverage](https://codecov.io/gh/elilillyco/pytest-wdl/branch/master/graph/badge.svg)](https://codecov.io/gh/elilillyco/pytest-wdl)\n[![Documentation Status](https://readthedocs.org/projects/pytest-wdl/badge/?version=latest)](https://pytest-wdl.readthedocs.io/en/latest/?badge=latest)\n\nThis package is a plugin for the [pytest](https://docs.pytest.org/en/latest/) unit testing framework that enables testing of workflows written in [Workflow Description Language](https://github.com/openwdl).\n\n## Dependencies\n\n* Python 3.6+\n* Java 1.8+\n* [Cromwell](https://github.com/broadinstitute/cromwell/releases/tag/38) JAR file\n* [Docker](https://www.docker.com/get-started) daemon (if your WDL tasks depend on Docker images)\n\nOther python dependencies are installed when you install the library.\n\n## Installation\n\n### Install from PyPI\n\n```commandline\n$ pip install pytest-wdl\n```\n\n### Install from source\n\nYou can to clone the repository and install:\n\n```\n$ make install\n```\n\nOr use pip to install from github:\n\n```commandline\n$ pip install git+https://github.com/elilillyco/pytest-wdl.git\n```\n\n### Install optional dependencies\n\nSome optional features of pytest-wdl have additional dependencies that are loaded on-demand. For example, to enable comparison of expected and actual BAM file outputs of a workflow, the [pysam](https://pysam.readthedocs.io/) library is required.\n\nThe following plugins require an \"extras\" installation:\n\n- Data types\n    - bam\n- URL schemes\n    - dx (DNAnexus)\n- Other\n    - progress (show progress bars when downloading files)\n\nTo install the dependencies for a data type that has extra dependencies:\n\n```\n$ pip install pytest-wdl[<data_type>]\n```\n\nTo do this locally, you can clone the repo and run:\n\n```commandline\n$ pip install -e .[<data_type>]\n```\n\nTo install pytest-wdl and **all** extras dependencies:\n\n```\n$ pip install pytest-wdl[all]\n```\n\n## Usage\n\nThe pytest-wdl plugin provides a set of fixtures for use with pytest. Here is a quick example:\n\n```python\n# test_variant_caller.py\ndef test_variant_caller(workflow_data, workflow_runner):\n    inputs = workflow_data.get_dict(\"bam\", \"bai\")\n    inputs[\"index\"] = {\n        \"fasta\": workflow_data[\"index_fa\"],\n        \"organism\": \"human\"\n    }\n    expected = workflow_data.get_dict(\"vcf\")\n    workflow_runner(\n        \"variant_caller.wdl\",\n        inputs,\n        expected\n    )\n```\n\nThis test will execute a workflow (such as the following one) with the specified inputs, and will compare the outputs to the specified expected outputs.\n\n```wdl\n# variant_caller.wdl\nversion 1.0\n\nstruct Index {\n  File fasta\n  String organism\n}\n\nworkflow call_variants {\n  input {\n    File bam\n    File bai\n    Index index\n  }\n  ...\n  output {\n    File vcf = variant_caller.vcf\n  }\n}\n```\n\nInput and output data are defined in a `test_data.json` file in the same directory as your test script:\n\n```json\n{\n  \"bam\": {\n    \"url\": \"http://example.com/my.bam\"\n  },\n  \"bai\": {\n    \"url\": \"http://example.com/my.bam.bai\"\n  },\n  \"index_fa\": {\n    \"name\": \"chr22.fasta\"\n  },\n  \"vcf\": {\n    \"url\": \"http://example.com/expected.vcf.gz\",\n    \"type\": \"vcf\",\n    \"allowed_diff_lines\": 2\n  }\n}\n```\n\nFor details, [read the docs](https://pytest-wdl.readthedocs.io).\n\n## Contributing\n\nTo develop pytest-wdl, clone the repository and install all the dependencies:\n\n```commandline\n$ git clone https://github.com/EliLillyCo/pytest-wdl.git\n$ pip install -r requirements.txt\n```\n\nTo run the full build and unit tests, run:\n\n```commandline\n$ make\n```\n\n## Support\n\npytest-wdl is *not* an official product of Eli Lilly or DNAnexus. Please do *not* contact these companies (or any employees thereof) for support. To report a bug or feature request, please open an issue in the [issue tracker](https://github.com/EliLillyCo/pytest-wdl/issues).",
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