lilab-bcb / altocumulus

Command line tool for submitting WDL jobs to Terra or Cromwell server.

https://altocumulus.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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============== Altocumulus

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Command line utilities for running workflows on Terra <https://app.terra.bio> or Cromwell <https://cromwell.readthedocs.io> 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 <https://api.firecloud.org/>_
Dockstore Swagger <https://dockstore.org/api/static/swagger-ui/index.html>_
FireCloud Service Selector <https://github.com/broadinstitute/fiss> (FISS). In particular, fiss/firecloud/api.py <https://github.com/broadinstitute/fiss/blob/master/firecloud/api.py>.