We have all of our sequencing files for WGS and RNA-seq stored in the genomics platform of the Broad and we only have paths to these files. I am wondering how to upload these files to the Firecloud?
What is the storage setup you have currently? Are these paths gs:// paths or are they stored on a local file system C:// or cluster (like gsa)?
If they are gs:// paths, then it is simply a matter of setting up your data model in FireCloud. These sound like samples, so you'd include the gs:// paths in your sample metadata table. You can read here about how to set that up.
If they are local or on a cluster, then you will need to upload the data to a Google bucket to get a gs:// path. Then you follow the instructions above to set up your data model. You can read about how to upload your data to a bucket here.
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