Is it possible to access arbitrary environmental variables inside a nextflow config?

env("VAR_NAME")

should do it, I think

Oh awesome, that makes my life much easier

You can also use the variables in strings, just like in `bash`:

singularity {
    enabled    = true
    // /tmp is often too small -> redirect to scratch:
    runOptions = "-B /scratch/$USER:/tmp"
}

env {
    SINGULARITY_TMPDIR   = "/scratch/$USER/singularity/tmp"
    SINGULARITY_CACHEDIR = "/scratch/$USER/singularity/cache"
}

(Obviously that works also with other variables besides

$USER

, these are just my use cases.) Be sure to to use double quotes to ensure expansion.

Oh really? I had just assumed that wouldn't work since it's so rare to see

It works for me. One thing to be careful about is when those expressions are evaluated. E.g.

$USER

is not likely to change over the run of a pipeline, but

$HOSTNAME

is likely different between the point where you start the pipeline and where a particular process is run. I think you can use closures (

{ ... }

) to control that.

This is for some on-prem infra, we want to tag k8s executor jobs/pods with the user creating them as an annotation for easier tracking, this isn't for any specific workflow so I'm not concerned about flow etc

Pretty sure the implicit access is not recommended now and that you should be using

system.getEnv

or

env

(docs - I think they are a bit confusing on the new best practice though personally)