Package: pytest-wdl
This package is a plugin for thepytestunit testing framework that enables testing of workflows written inWorkflow Description Language.DependenciesPython 3.6+At least one of the supported workflow engines:Miniwdl- automatically installed as a dependency of pytest-wdlCromwellJAR fileCromwell Server: Any Cromwell instance remotely running in Server modedxWDLJAR fileJava-based workflow engines (e.g. Cromwell and dxWDL) require a Java runtime (typically 1.8+)If your WDL tasks depend on Docker images, make sure to have theDockerdaemon runningOther python dependencies are installed when you install the library.InstallationInstall from PyPI$ pip install pytest-wdlInstall from sourceYou can to clone the repository and install:$ make installOr use pip to install from github:$ pip install git+https://github.com/elilillyco/pytest-wdl.gitInstall optional dependenciesSome optional features of pytest-wdl have additional dependencies that are loaded on-demand.The plugins that have extra dependencies are:dx: Support for DNAnexus file storage, and for the dxWDL executor.bam: More intelligent comparison of expected and actual BAM file outputs of a workflow than just comparing MD5 checksums.http: Support for executors that use HTTPS protocol to communicate with a remote server (e.g. Cromwell Server)yaml: Support using YAML for configuration and test data files.progress: Show progress bars when downloading remote files.To install a plugin's dependencies:$ pip install pytest-wdl[<plugin>]To do this locally, you can clone the repo and run:$ pip install -e .[<data_type>]To install pytest-wdl andallextras dependencies:$ pip install pytest-wdl[all]UsageThe pytest-wdl plugin provides a set of fixtures for use with pytest. Here is a quick example that tests the following workflow.# variant_caller.wdl
version 1.0

import "variant_caller.wdl"

struct Index {
  File fasta
  String organism
}

workflow call_variants {
  input {
    File bam
    File bai
    Index index
  }
  
  call variant_caller.variant_caller {
    input:
      bam=bam,
      bai=bai,
      index=index
  }

  output {
    File vcf = variant_caller.vcf
  }
}Inputs and expected outputs are defined in atest_data.jsonfile in the same directory as your test script:{"bam":{"url":"http://example.com/my.bam"},"bai":{"url":"http://example.com/my.bam.bai"},"index_fa":{"name":"chr22.fasta"},"vcf":{"url":"http://example.com/expected.vcf.gz","type":"vcf","allowed_diff_lines":2}}You can write the test code in Python, or - in most cases - you can define the test in a JSON or YAML file instead. The following Python and JSON code define exactly the same test. This test will cause the workflow to be run with the specified inputs, and the outputs will be compared to the specified expected outputs.# test_variant_caller.pydeftest_variant_caller(workflow_data,workflow_runner):inputs=workflow_data.get_dict("bam","bai")inputs["index"]={"fasta":workflow_data["index_fa"],"organism":"human"}expected=workflow_data.get_dict("vcf")workflow_runner("variant_caller.wdl",inputs,expected)#test_variant_caller.json{"tests":[{"name":"test_variant_caller","wdl":"variant_caller.wdl","inputs":{"bam":"bam","bai":"bai","index":{"fasta":"index_fa","organism":"human"}},"outputs":{"vcf":"vcf"}}]}For details,read the docs.ConfigurationYou can get started with pytest-wdl with no configuration required. However, some advanced features can be configured via environment variables, fixture functions, and/or a config file. To get started, copy one of the following example config files to$HOME/.pytest_wdl_config.jsonand modify as necessary:simple: Uses only the miniwdl executormore complex: Uses both miniwdl and Cromwell; shows how to configure proxies and headers for accessing remote data files in a private repositorySee themanualfor more details on configuring pytest-wdl.ContributingIf you would like to contribute code to pytest-wdl, please fork the repository and submit your changes via pull request.To get started developing pytest-wdl, first install all the development requirements:$ git clone https://github.com/EliLillyCo/pytest-wdl.git
$ make install_development_requirementsTo run the full build and unit tests, run:$ makeSupportpytest-wdl isnotan official product of Eli Lilly or DNAnexus. Please donotcontact these companies (or any employees thereof) for support. To report a bug or feature request, please open an issue in theissue tracker.