Add option to use cwltool as runner (RAP-6)
Created a new class, CWLRunner
, with two child classes, CWLToolRunner
and ToilRunner
, and a factory method create_cwl_runner()
, which returns an instance of either of the two child classes. The logic to configure a given runner has been moved from rapthor/lib/operation.py
to the new file rapthor/lib/cwlrunner.py
. A new parset key cwl_runner
has been added. By default, toil
will be used as CWL runner, but this can now easily be overridden by adding the option cwl_runner
to the [cluster]
section of the Rapthor parset file.
Closes RAP-6