amazon-genomics-cli

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Nextflow version

1

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) **Describe the Bug** [//]: # (Please describe the behavior that you are seeing...

jmbaek

feat: Support and use Toil 5.8's WES task output

1

Issue #, if available: **Description of Changes** [//]: # (A description of the change that you made and the new user experience that it creates) As of https://github.com/DataBiosphere/toil/pull/4166, due to...

adamnovak

Issue #, if available: #458 **Description of Changes** Added CLI support for requesting the use of `PRIVATE` ApiGateway endpoints when activating an account so that all contexts subsequently deployed will...

markjschreiber

Clarify how inputFileUrls are handled for engines other than Cromwell

1

See specific instructions for Cromwell here: https://aws.github.io/amazon-genomics-cli/docs/concepts/workflows/#manifestjson-structure How is this handled for miniWDL and others? I can see wanting having two input JSON files, one for a static set (e.g....

nh13

Support concurrent workflows with different manifests

6

As [described here](https://github.com/aws/amazon-genomics-cli/issues/474#issuecomment-1190524749), I’d like AGC to support running multiple workflows in the same context: > …the MANIFEST.json with a per-workflow inputFileURLs specified in the MANIFEST.json is packaged with the...

nh13

Task Stdout not written to cloud watch for MiniWDL tasks

8

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) **Describe the Bug** When running a workflow using a MiniWDL context, any task...

patmagee

Runs are exposed across contexts via the WES API

1

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) **Describe the Bug** If a user has two MiniWDL contexts deployed in the...

patmagee

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) **Describe the Bug** An `agc account deactivate` did not deactivate the account, but...

coverbeck

GPU support for running WDL jobs

1

Hello, Cromwell has runtime attributes such as `gpuCount`, `gpuType` and `nvidiaDriverVersion` (https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#gpucount-gputype-and-nvidiadriverversion), but it seems they only work for GCP. So I'm wondering if AGC, [genomics workflows](https://github.com/aws-samples/aws-genomics-workflows), or [Cromwell-AWS](https://github.com/henriqueribeiro/cromwell) provides...

yihming

agc context deploy --context myContext fails due to A load balancer cannot be attached to multiple subnets in the same Availability Zone

18

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) **Describe the Bug** Following the instructions to get started, when I run ```...

golharam