From 002c7c0d508d4d18f9737d0fdca6f251d01b966a Mon Sep 17 00:00:00 2001 From: Heather Ward Date: Tue, 4 Jul 2023 11:29:34 -0400 Subject: [PATCH] Allow user to override container registry --- README.md | 1 + backends/hpc/inputs.hpc.json | 3 +-- workflows/main.wdl | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 86d80b97..e1e19721 100644 --- 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'. | | | 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 index 1fd5d971..f367ecf8 100644 --- 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 index cc86e098..e292cfc2 100644 --- 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"} } }