Can process pod declaration merge with config pod declaration?

[alanbchristie]

I have a nextflow.config with a process pod declaration, i.e. something like this...

process {
  pod = [ [nodeSelector: 'example.com/purpose=core'],
          [label: 'example.com/instance-id',
           value: 'instance-7be5e19c-02c9-427f-a840-581728d46397'] ]
}

As you can see, it defines a nodeSelector and a label.

But, if I run a process that also defines a pod declaration, with different (non-overlapping) properties, like this...

process combine {

    pod imagePullSecret: 'example-com-secret'
    container 'registry.gitlab.com/example/example:stable'

    [...]
}

...the pod declaration in the nextflow.config appears to be lost - i.e. the nodeSelector and labels are not applied to the process pod.

So...

1. Is there a way to combine (merge) the pod declarations?
2. ...if not, would it actually be useful to others? i.e. does this warrant a bug/feature request?
3. ...if not, can the documentation be adjusted to make it clear that in-process declarations replace configured declarations with a clear example?

[pditommaso]

This is the expected behaviour, likely it should be documented better.

Regarding this specific use case, we are working on improving the support for labels. We'll take in consideration your point.

[alanbchristie]

Thank you. The ability to merge pod declarations with the config would provide an extremely flexible way to configure the workflow.

For our specific case, as we are simply setting a Kubernetes imagePullSecret, I realise that we can avoid the config pod declaration from being lost by attaching the secret(s) to the ServiceAccount rather than via the pod. That way the config pod declaration is not lost.