You can run the following DQL to get the workflows currently in progress in your repository:
SELECT w.r_object_id, d.r_object_id, d.object_name AS doc_name, d.document_status AS doc_status, w.object_name AS workflow_name, w.supervisor_name AS workflow_supervisor FROM dm_workflow w, dm_document d WHERE d.r_object_id IN (select distinct r_component_id from dmi_package where r_workflow_id = w.r_object_id);
If you want to remove running workflow's from the system (for instance during a system upgrade) you can run the following API commands with the workflow IDs returned from the above DQL:
halt,c,<r_object_id of workflow>
abort,c,<r_object_id of workflow>
destroy,c,<r_object_id of workflow>