amazon-genomics-cli

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Support ARM based instance types or document that they cannot be used

1

**Description** I only discovered that ARM based instance types are not supported when I tried to deploy a context with [M6g machines](https://aws.amazon.com/ec2/instance-types/m6g/) and it failed with the following error message:...

AsierGonzalez

**Description** Version 7.11 includes a rework of resource handling for job groups. This would be super helpful in the context of AGC considering that the job submission overhead can add...

ElDeveloper

--inputsFile is not being passed to miniwdl run

13

[//]: # (Please do not include your AWS account or credentials as part of the bug request.) The parameters specified in the JSON given to `--inputsFile` are not being propagated...

nh13

Add retry mechanism for Snakemake workflows running in spot contexts

1

[//]: # (Before raising the feature request, please check to see if an existing feature request already exists.) **Description** Running in a spot context is very convenient, unfortunately when an...

ElDeveloper

feat: Added option to pass custom WES Adapter environment variables

1

Issue #: https://github.com/aws/amazon-genomics-cli/issues/396 **Description of Changes** [//]: # This adds option to pass custom environment variables into WES Adapter [//]: # This adds option to pass custom environment variables into...

kankou-aliaksei

Issue #, if available: **Description of Changes** Added a port of `words-with-vowels` workflow in CWL **Description of how you validated changes** * `agc context deploy myContext` * `agc workflow run...

markjschreiber

Setting environment variables in workflow engine container

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miniwdl allows any of its configuration options to be overridden by environment variables ([details](https://miniwdl.readthedocs.io/en/latest/runner_reference.html?highlight=errata#configuration)). This is often a more-convenient way to tune them compared to editing a configuration file (also...

mlin

"results" folder not stored when using nextflow engine

1

### Discussed in https://github.com/aws/amazon-genomics-cli/discussions/481 Originally posted by **MrOlm** June 13, 2022 Hello, After a Nextflow run there is usually a "results" folder created, but that output is uploaded to AWS...

MrOlm

WES Endpoint URL returned by `agc context describe` is incomplete

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...

wleepang

`agc logs workflow` output does not use the configured formatter

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...

wleepang