How to use asset bundles in a WDL workflow?

[e-dorigatti]

My workflow needs custom code and other resources to run. I have a prototype working locally via WDL and a docker image with all the requirements. I now created an asset bundle with those requirements and I was hoping to use it as demonstrated in this example, however I did not find any way of specifying this asset bundle when building the workflow. I tried via the -extras option, but runSpec.assetDepends does not seem to be accepted.

I am aware that I can upload the docker image to dnanexus and use it directly but I would prefer to avoid it since it's 15 GBs worth of data and libraries an it takes quite some time to save and upload, and this quickly becomes a hassle as we are actively developing and frequently updating this workflow. Using a public docker registry is also not an option since the image contains protected company assets, and our private registry is obviously not accessible from the outside.

What is the best way to proceed?

[emiloslavsky]

asset bundles are used with DNAnexus-native applets/apps, not WDL tasks.

WDL encourages the use of container images for runtime environment specification (e.g. from https://docs.openwdl.org/language-guide/tasks.html#the-requirements-section)

The requirements section  allows you to specify runtime requirements for a task. By far the most common use of requirements is to specify a container for your task to run within. This ensure that the task remains portable across multiple execution environments and is always recommended.

You can try passing the asset bundle as an argument to your WDL task and installing it within the code section of the task as a workaround.