Post-processing & Lightweight Updates To pipeline Output
CWL files and workflows to accompany the helix_filters_01 repo.
Development and testing takes place via the test suite.
Make sure that you have copies of the Singularity containers used cached locally
make singularity-pull
make singularity-pull-dev
make singularity-pull-facets
The included test suite can be run with:
make test
It typically takes about 45 minutes to run all included tests
- NOTE: tests require data sets that are pre-saved on the
junoserver
An extra recipe is included which can run the tests in parallel, for example to run 8 tests at once you can use this command:
make test3 -j 8
For development purposes, it is helpful to be able to run only a specific test case, or subset of tests.
To do this, first enter an interactive bash session with the environment populated;
make bash
The run the script with the tests you are interested in, such as;
python tests/test_workflow_cwl.py
You can further select which test case(s) from the script you wish to run by adding their labels as args;
python tests/test_workflow_cwl.py TestClassName
python tests/test_workflow_cwl.py TestClassName.test_function