Add support for Fargate resource type for AWS Batch

[pditommaso]

This PR adds support Fargate resource type for AWS Batch executor.

[ShanWeera]

@pditommaso hey there Paolo!. Just stumbled upon this after hours of trying to get Nextflow working with AWS Batch + Fargate. Fargate support would be really great to have so really appreciate the work you have put in here.

Going from what you mentioned over at: https://groups.google.com/g/nextflow/c/JFneg8d3x2w/m/EjYGXUubCQAJ

The problem with Fargate is that it does not allow host mounts which NF needs to access the aws cli tool without installing it in the container.

Have you been able to find a workaround for this limitation?

As an aside, I feel the documentation does not make it very clear that Fargate is in fact not supported by Nextflow. Fargate is actually the default selection when creating AWS Batch job definitions and queues, and it is arguably the most convenient way to get started with AWS Batch (among other advantages).

All this to suggest that it might be worth it to explicitly mention this limitation somewhere in the documentation, as I imagine many people would go with Fargate just to realise later that this is not supported (at least for the moment).

[bentsherman]

Don't think we've found a workaround yet. We either need to be able to mount the AWS CLI or use Fusion, but there also we are waiting on this proposal to make that possible.

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