linsalrob / commonworkflowlanguage

CWL codes and examples for searchSRA.org

Common Workflow Language Examples

These are some common workflow language examples that we are using for search sra. They specify different things that we can do.

Getting started

Before you begin, you'll need a CWL parser. At the moment we're using cwltool installed in a Python 3.6 virtual environment.

Testing your configs

I use JSON for my configs rather than YAML (because I prefer JSON). However, it can be persnickity to test the config files if you edit them manually.

I use a command like this one:

python3 json_keys.py -f minimap2.cwl

to test whether the JSON file is in the correct format. Very quickly you will get to learn the errors in your JSON ways!

You can download json_keys.py from the EdwardsLab git repo.