Accomodating GCP error codes in docs and workflow design.

[r0f1]

Hi, I am referring to this section: https://www.nextflow.io/docs/latest/google.html#preemptible-instances

Yes it is true, that if a VM gets preemted, the error code is 14, but that is not the whole truth.

According to the Google Life Sciences documentation it can be 8, 10 or 14. See: https://cloud.google.com/life-sciences/docs/troubleshooting, Section: Retrying after encountering errors

It would be nice to add that info to the docs as well.

[abhi18av]

Hi @r0f1 , thank you for your suggestion :)

Since the nature of these error codes is independent of the NF example mentioned in the docs, perhaps it'd be more appropriate to add a TIP in the docs to refer the official error code docs from GCP https://cloud.google.com/life-sciences/docs/troubleshooting#error_codes

This might be safer, since GCP might decide to add / update the error codes in future.

What do you think?

[r0f1]

Sure, add it as a TIP. Just add it in some way such that developers who want to use preemptible machines know what to look out for. Given that the default value of google.lifeSciences.preembtible is true, I think this is especially important. Here is what I did by the way, but maybe there is a more elegant way:

# nextflow.config
process {
    withLabel: foo {
        executor = "google-lifesciences"
        errorStrategy = {(task.exitStatus==8 || task.exitStatus==10 || task.exitStatus==14) ? 'retry' : 'terminate'}
        maxRetries = 10
    }
}

[abhi18av]

Yup, that makes sense 👍

However, I also think that you could probably extract that out as a reusable function like shown here .

[abhi18av]

@r0f1 , with this #1914 we've added a tip regarding the GLS error codes.