SBG CWL runner AKA CWL E. Coyote AKA Coyote

This code is in the planning stage

CWL E. Coyote (/Kwɪ’li E kaɪˈoʊti/), “Coyote” for short, is A CWL Runner for the Seven Bridges Genomics cloud platform. It supplies a cwl-runner style interface that runs tasks via the Seven Bridges API

What’s in a name?: Wile E. Coyote

Dependencies

• sevenbridges-python for API access to SBG Platform

Run the cwl conformance tests

(Check the language website for details on setting up the conformance tests. Use ./run_test.sh --help to get more detailed usage information about the conformance test manager.)

To run conformance tests with the SBG platform and sbg-cwl-runner do:

cd cwl-language-directory
./run_test.sh -j100 RUNNER=sbg-cwl-runner EXTRA=--project="my-cwl-test-project"

How it works

1. Wiley old CWL E. uploads the supplied CWL workflow (if needed) to the platform, first resolving any dependencies
2. It uploads the test files refered to in the job file
3. It creates a new task based on the job file and runs it
4. It waits until the task is done and retrieves the stderr log and the output object