Add check if parameters are specified via .config file to pipeline template

[grst]

Description of feature

Specifying parameters via -c custom.config can make problems with DSL2 workflows. The corresponding documentation was added in #2173.

I'm afraid there's still a considerable number of users following this practice, and in the worst case this may lead to incorrect results because parameters are silently ignored. Having a loud warning (or even error) when a workflow with a custom config file is started would be great!

I prototyped this snipped, and it seems to work in principle. However, it would need some tuning that it doesn't raise an error for the config file that defines the default parameters.

def check_config_files(workflow) {
    for (config_file in workflow.configFiles) {
        if (file(config_file).text.contains("parameters")) {
            println "WARNING: Do not specify parameters via a .config file."
        }
    }
}

workflow {
    check_config_files(workflow)
}

Maybe someone can take this on at the hackathon?

CC @jfy133

[drpatelh]

parameters -> params

The ideal situation here would be to load each of these configs and see whether the params object is empty or not. Looking for strings like params could go wrong too?

[drpatelh]

This also assumes users will read STDOUT which they probably won't in the Cloud.

[drpatelh]

See nf-core/rnaseq#972 for how it has been added to rnaseq and viralrecon for now. We can take what we want from this and/or update too.

[grst]

This also assumes users will read STDOUT which they probably won't in the Cloud.

unless it aborts the pipeline? But aborting would definitely be too risky when doing a simple string search.

See nf-core/rnaseq#972 for how it has been added to rnaseq and viralrecon for now. We can take what we want from this and/or update too.

👍, but this also leads to a few false-positives? E.g. providing process withName: via config file is completely legit.

Loading the config files would be perfect... is there a way to access individual config files in nextflow?

[maxulysse]

yes, but I think the warning message is clear enough

[grst]

yes, but I think the warning message is clear enough

agree, and it's already better than my naive check for "params".

My point was: if we had a reliable way of detecting that params were specified via config file, I'd consider a failure instead of a warning.