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[WX-1595] Specify gcp_batch_gcs_root as temporary directory in docs…
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… for GCP Batch Backend (#7435)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
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@illusional @aednichols
illusional and aednichols committed May 15, 2024
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4 changes: 2 additions & 2 deletions docs/backends/GCPBatch.md
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Expand Up @@ -92,7 +92,7 @@ While technically not part of Service Account authentication mode, one can also

A [JSON key file for the service account](../wf_options/Google.md) must be passed in via the `user_service_account_json` field in the [Workflow Options](../wf_options/Google.md) when submitting the job. Omitting this field will cause the workflow to fail. The JSON should be passed as a string and will need to have no newlines and all instances of `"` and `\n` escaped.

In the likely event that this service account does not have access to Cromwell's default google project the `google_project` workflow option must be set. In the similarly likely case that this service account can not access Cromwell's default google bucket, the `jes_gcs_root` workflow option should be set appropriately.
In the likely event that this service account does not have access to Cromwell's default google project the `google_project` workflow option must be set. In the similarly likely case that this service account can not access Cromwell's default google bucket, the `gcp_batch_gcs_root` workflow option should be set appropriately.

For information on the interaction of `user_service_account_json` with private Docker images please see the `Docker` section below.

Expand Down Expand Up @@ -152,7 +152,7 @@ The output of this script will be written to a `monitoring.log` file that will b
**Google Cloud Storage Filesystem**

On the Google Batch backend the GCS (Google Cloud Storage) filesystem is used for the root of the workflow execution.
On the Local, SGE, and associated backends any GCS URI will be downloaded locally. For the Google backend the `jes_gcs_root` [Workflow Option](../wf_options/Google) will take
On the Local, SGE, and associated backends any GCS URI will be downloaded locally. For the Google backend the `gcp_batch_gcs_root` [Workflow Option](../wf_options/Google) will take
precedence over the `root` specified at `backend.providers.JES.config.root` in the configuration file. Google Cloud Storage URIs are the only acceptable values for `File` inputs for
workflows using the Google backend.

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2 changes: 1 addition & 1 deletion docs/wf_options/Google.md
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Expand Up @@ -6,7 +6,7 @@ These workflow options provide Google-specific information for workflows running

| Keys | Possible Values | Description |
|------------------------------------|-----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `jes_gcs_root` | `string` | Where outputs of the workflow will be written. Expects this to be a GCS URL (e.g. `gs://my-bucket/workflows`). If this is not set, this defaults to the value within `backend.jes.config.root` in the [Configuration](../Configuring). |
| `jes_gcs_root` | `string` | Where outputs of the workflow will be written. Expects this to be a GCS URL (e.g. `gs://my-bucket/workflows`). If this is not set, this defaults to the value within `backend.jes.config.root` in the [Configuration](../Configuring). (Note this is called `gcp_batch_gcs_root` on the GCPBatch backend.) |
| `google_compute_service_account` | `string` | Alternate service account to use on the compute instance (e.g. `my-new-svcacct@my-google-project.iam.gserviceaccount.com`). If this is not set, this defaults to the value within `backend.jes.config.genomics.compute-service-account` in the [Configuration](../Configuring) if specified or `default` otherwise. |
| `google_project` | `string` | Google project used to execute this workflow. |
| `auth_bucket` | `string` | A GCS URL that only Cromwell can write to. The Cromwell account is determined by the `google.authScheme` (and the corresponding `google.userAuth` and `google.serviceAuth`). Defaults to the the value in [jes_gcs_root](#jes_gcs_root). |
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