Command line utilities for running workflows on Terra or Cromwell including:
- Run a Terra method, and bulk add/delete methods on Terra.
- Submit WDL workflow jobs to a sever running Cromwell, as well as check jobs' status, abort jobs, and get logs.
- Replace local file paths with remote Cloud (Google Cloud or Amazon AWS) bucket URIs, and automatically upload referenced files to Cloud buckets.
- Parse monitoring log files to determine optimal instance type and disk space.
Important tools used by Altocumulus:
- FireCloud Swagger
- Dockstore Swagger
- FireCloud Service Selector (FISS). In particular, fiss/firecloud/api.py.