README.md

Testing

Requirements

• Pytest-workflow
• csvtk for processing of Achab Excel (path to exe hard-defined in tests/wwwachab/run_and_specials.sh)

Directories organization

tests sub-dir contains 1 test_my_workflow.yaml file for each tested workflow or sub-workflow

Test datas for each workflow are expected to be under tests/my_workflow/

Run tests

General syntax

pytest \
	--verbose \
	--git-aware \
	tests/

Explanations (see documentation for details) :

• With --basetemp=, pytest-wf will run test inside /scrath/<TEST_NAME>
• Input JSON are configured so that everything lies inside /scrath/<TEST_NAME> (cromwell-exec + pipeline output)
• Due to --keep-workflow-wd option, all dirs created by pytest-wf must be be deleted manually afterwards
• Remove --git-aware if uncommited changes or outside git repo (otherwise error)

Available tests

# Show Achab version:
pytest \
        --tag version \
        --verbose \
        --git-aware \
        tests/test_wwwachab.yaml

# Show Achab help:
pytest \
        --tag help \
        --verbose \
        --git-aware \
        tests/test_wwwachab.yaml

# Downsampled (only chr22) exome VCF with minimal Achab params:
pytest \
        --tag solo --tag exome --tag downsampled --tag minimal \
        --verbose \
        --git-aware \
        tests/test_wwwachab.yaml

# Downsampled (only chr22) exome VCF with Achab params used in production:
pytest \
        --tag solo --tag exome --tag downsampled --tag prod \
        --verbose \
        --git-aware \
        tests/test_wwwachab.yaml

# Full trio of exome (with params used in production):
pytest \
        --tag trio --tag exome --tag full --tag prod \
        --verbose \
        --git-aware \
        tests/test_wwwachab.yaml