How to use DRS URIs in a workflow that runs docker image with a tool inside
Hi,
This is probably trivial but as I am new to terra I was wondering if anyone could share an examples (or point me to one) where I can see how to properly use DRS URIs from inside a docker image. The image contains a tool to which, on my local server, I pass an input file via '-v' . Example (pseudo):
```
docker run --rm -i -v /path/to/data1:/opt/mnt/data -v /path/to/input:/opt/mnt/input mydoc:1.0.0 /bin/bash/ -c " mytool -r /opt/mnt/data -i /opt/mnt/input > out"
```
where `data1` is a resource directory and `input` is a file.
My question is, how would this be implemented in a wdl script where i need to provide DRS URIs as an input to my tool?
Thank you
Comments
1 comment
Hi Robert,
If you are running the WDL on Terra, you should be able provide the DRS URI as a regular input and Terra/Cromwell will be able to localize the file to your task's VM (assuming you have access to the file) and run whatever tool you've installed in your Docker.
For more information, please see the following support articles on DRS:
Overview: Interoperable data (GA4GH DRS URIs)
How to use DRS URIs in a workflow (GCP)
Best,
Samantha
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