No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.circleci
examples
testing_functions
workflows4regtests/basic_examples
.gitattributes
.gitignore
README.md
__init__.py
altair_plots.py
container_generator.py
cwl_generator.py
testrunner.py
workflowregtest.py

README.md

Regression tests

Preparing workflow for testing

  • each workflow should have a separate dictionary under workflows4regtests
  • the workflow with command line interface should be in the workflow subdirectory
  • all input data needed to run the workflow should be under the data_input subdirectory
  • all reference results should be saved in the data_ref subdirectory
  • each workflow should have parameters.json to describe environment, input data, script and command to run the workflow, and chosen tests for the workflow outputs, e.g.
{
    "command": "python",
    "env": {
        "base": [
            "debian:stretch",
            "ubuntu:17.04"
        ],
        "conda_env_yml": [
            "environment_py2.yml",
            "environment_py3.yml"
        ],
        "fsl": [
            "5.0.9",
            "5.0.10"
        ]
    },
    "inputs": [
        [
            "string",
            "--key",
            "11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA"
        ],
        [
            "int",
            "-n",
            "1"
        ]
    ],
    "script": "run_demo_workflow.py",
    "tests": [
        {
        "file": "output/metaflow/AnnArbor_sub16960/save_json/segstats.json", 
        "script": "check_output.py", 
        "name": "test"
        }
    ]
}