Allow user to override container registry

PacificBiosciences · Jul 4, 2023 · 002c7c0 · 002c7c0
1 parent f3aa8b3
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -227,6 +227,7 @@ These files are hosted publicly in each of the cloud backends; see `backends/${b
 | String? | zones | Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'. | <ul><li>[Determining available zones in AWS](backends/aws/README.md#determining-available-zones)</li><li>[Determining available zones in GCP](backends/gcp/README.md#determining-available-zones)</li></ul> |
 | String? | aws_spot_queue_arn | Queue ARN for the spot batch queue; required if backend is set to 'AWS' and `preemptible` is set to `true` | [Determining the AWS queue ARN](backends/aws/README.md#determining-the-aws-batch-queue-arn) |
 | String? | aws_on_demand_queue_arn | Queue ARN for the on demand batch queue; required if backend is set to 'AWS' and `preemptible` is set to `false` | [Determining the AWS queue ARN](backends/aws/README.md#determining-the-aws-batch-queue-arn) |
+| String? | container_registry | Container registry where workflow images are hosted. If left blank, [PacBio's public Quay.io registry](https://quay.io/organization/pacbio) will be used. | |
 | Boolean | preemptible | If set to `true`, run tasks preemptibly where possible. On-demand VMs will be used only for tasks that run for >24 hours if the backend is set to GCP. If set to `false`, on-demand VMs will be used for every task. Ignored if backend is set to HPC. | \[true, false\] |
 
 # Workflow outputs

diff --git a/backends/hpc/inputs.hpc.json b/backends/hpc/inputs.hpc.json
@@ -92,6 +92,5 @@
   "humanwgs.glnexus_mem_gb": "Int (optional, default = 30)",
   "humanwgs.run_tertiary_analysis": "Boolean (optional, default = true)",
   "humanwgs.backend": "HPC",
-  "humanwgs.zones": "String",
-  "humanwgs.preemptible": "Boolean"
+  "humanwgs.preemptible": true
 }
diff --git a/workflows/main.wdl b/workflows/main.wdl
@@ -35,7 +35,8 @@ workflow humanwgs {
 			backend = backend,
 			zones = zones,
 			aws_spot_queue_arn = aws_spot_queue_arn,
-			aws_on_demand_queue_arn = aws_on_demand_queue_arn
+			aws_on_demand_queue_arn = aws_on_demand_queue_arn,
+			container_registry = container_registry
 	}
 
 	RuntimeAttributes default_runtime_attributes = if preemptible then backend_configuration.spot_runtime_attributes else backend_configuration.on_demand_runtime_attributes
@@ -145,6 +146,7 @@ workflow humanwgs {
 		zones: {help: "Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'"}
 		aws_spot_queue_arn: {help: "Queue ARN for the spot batch queue; required if backend is set to 'AWS'"}
 		aws_on_demand_queue_arn: {help: "Queue ARN for the on demand batch queue; required if backend is set to 'AWS'"}
+		container_registry: {help: "Container registry where workflow images are hosted. If left blank, PacBio's public Quay.io registry will be used."}
 		preemptible: {help: "Where possible, run tasks preemptibly"}
 	}
 }