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

docs/source/parset.rst

@@ -339,3 +339,18 @@ The available options are described below under their respective sections.
 
             - when :term:`use_mpi` = ``True`` under the :ref:`parset_imaging_options`
               section and ``dir_local`` is not on a shared filesystem.
+
+    cwl_runner
+        CWL runner to use. Currently supported runners are: cwltool and toil (default).
+        Toil is the recommended runner, since it provides much more fine-grained control
+        over the execution of a workflow. For example, Toil can use Slurm to automatically
+        distribute workflow steps over different compute nodes, whereas CWLTool can only
+        execute workflows on a single node. With CWLTool you also run the risk of
+        overloading your machine when too many jobs are run in parallel. For debugging
+        purposes CWLTool outshines Toil, because its logs are easier to understand.
+
+    debug_workflow
+        Debug workflow related issues. Enabling this will require significantly more
+        disk space. The working directory will never be cleaned up, stdout and stderr
+        will not be redirectied, and log level of the CWL runner will be set to DEBUG.
+        Use this option with care!