pluto-cwl

Post-processing & Lightweight Updates To pipeline Output

CWL files and workflows to accompany the helix_filters_01 repo.

Test Suite

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 juno server

Parallel Test Suite

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

Single Test

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