Use Kubernetes executor for Nextflow pipelines instead of SGE

[mike-miroliubov]

Background
Just an idea:
Currently SGE executor is being used for Nextflow pipelines. For this sake, an auto-scaling SGE cluster has to be deployed by cloud pipeline (over Kubernetes cluster). This works fine, however, introduces a redundant level of orchestration. Plus, SGE's scheduling, error codes and etc are far from perfect. On the other hand, Nextflow natively supports using Kubernetes as an executor and we can leverage this support to get rid of SGE in this case.

Approach
Use Nextflow built-in Kubernetes support:
https://www.nextflow.io/docs/edge/executor.html#kubernetes
https://www.nextflow.io/docs/edge/kubernetes.html
https://www.nextflow.io/docs/edge/config.html#scope-k8s
and, probably,
https://www.nextflow.io/docs/edge/kubernetes.html#running-in-a-pod

It should be possible to bound nodes for Nextflow cluster with namespace or node labels, using NF k8s config.

[sidoruka]

@K-I-T-E thanks for this proposal. We've considered Kube executor as an option in the initial implementation (See #291). But in the end, we've chosen to follow the strategy:

• Use SGE executor as a quick start (easy to implement and port existing workflows)
• Add GA4GH TES Executor option, once it matures up (we do have a TES wrapper implementation in place TES Support: Implementing adapter-service for TES #749). This one seems to be more "technology-agnostic", compared to both SGE and Kube

To my mind, implementation of the direct Kube executor support won't bring much of the value to the platform but requires a lot of engineering effort.

But definitely, there can be other valuable opinions. @mzueva @tcibinan any thoughts?