Mounting a Google Cloud Storage bucket in WDL workflow

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1

Hi.
I have used dsub to submit and run batch scripts in the cloud. (GitHub - DataBiosphere/dsub: Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.)

dsub allows a flag, – mount, to mounting a Google Cloud Storage bucket.

--mount RESOURCES=gs://mybucket

Inside the batch script, users can reference the mounted path using the environment variable, {RESOURCES}. This option avoids using literal values for the file location. I usually combine this option with an input file where the relative file paths for each sample file are stored. The script will take the input file and find those files on the bucket.

I wonder if WDL has this option, so I don’t need to spell out the entire file path on the cloud. Or WDL can access other files on the mounted storage bucket.
Thanks.

2

@truckload

I don’t think there is a pre-defined WDL variable for it. But one workaround is that you can grab the Bucket Name from the Dashboard and store it in the Workspace data table:

3

Thank you very much.