Cromwell's documentation on getting started with Google's genomics Pipelines API can be used to set up the resources needed to run the workflow.
Fill out any information missing in the inputs file.
See the inputs section of the singleton README for more information on the structure of the inputs.json file.
To determine available zones in GCP, run the following; available zones within a region can be found in the first column of the output:
gcloud compute zones list | grep <region>For example, the zones in region us-central1 are "us-central1-a us-central1-b us-central1c us-central1f".
Cromwell's documentation on getting started with Google's genomics Pipelines API can be used as an example for how to run the workflow.
GCP reference data is hosted in the us-west1 region in the bucket gs://pacbio-wdl. This bucket is requester-pays, meaning that users will need to provide a billing project in their Cromwell configuration in order to use files located in this bucket.
To avoid egress charges, Cromwell should be set up to spin up compute resources in the same region in which the data is located. If possible, add cohort data to the same region as the reference dataset, or consider mirroring this dataset in the region where your data is located. See Google's information about data storage and egress charges for more information.