I have a pipeline, which is written in WDL & runs with the help of Cromwell. I use Docker for containerization.
However, my container is dependent on huge (>100GB databases), which cannot be shipped with the image.
Is there an option to mount a directory from the host filesystem to a Docker while running Cromwell workflow? I found this functionality in snakemake, therefore I assume it is common, but I haven't found it in the docs yet.


1 Answer 1


Not an expert of WDL but looking at Cromwell documentation, there is a block in the configuration of Cromwell called submit-docker:

you'll need to modify the config block inside backend.providers in your Cromwell configuration. In particular, this block contains a key called submit-docker

In this example file, on line 420, it is possible to specify the mount option which is -v /path/you/need/to/mount:/path/in/docker/container (usually they are the same) to Docker command line. Setting it like that should work.

  • 1
    $\begingroup$ Thanks, I modified config and was able to mount directories! $\endgroup$
    – crusher083
    Commented Jan 17, 2022 at 11:57

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