also getting this warning:

Using `paramsHelp()` is not recommended. Check out the help message migration guide: <url>

I think the url is missing that I should check?

Ah crap I forgot to add it 😁

validation {
    failUnrecognisedParams = false
    lenientMode            = true
    defaultIgnoreParams    = [ 'cf_ploidy', 'genomes', 'igenomes_base', 'snpeff_db', 'test_data', 'vep_cache_version' ]
    showHiddenParams       = false
    help {
        enabled: true
        command: "nextflow run nf-core/sarek --input input_file.csv --outdir results"
    }
}

gives me: `ERROR ~ Unknown config attribute

<http://validation.help|validation.help>

-- check config file: /workspace/nf-core_sarek/nextflow.config` 🆘

You should use

=

instead of

:

in the config 😛

😄

Nothing ever goes right in the first try 😁

sorry for finding the only two things that are not working right away 😄 Is the migration guide relatively up to date? I am test running it with sarek now.

Thanks for reporting them! They shouldn't have been there 😁

showHiddenParams       = true

shouldn't this show the hidden parameters without

--showHidden

?

Yeah it should!

https://nextflow-io.github.io/nf-schema/latest/configuration/configuration/#help Can you try the new option for that? showHiddenParams is deprecated 😛

🤣 ok

So validation.help.showHidden 😛

that works

Okay cool! Can you open an issue about the old option? So I don't forget to fix it 😁

yes defaultIgnore also seems to be superseded by

ignoreParams

What do you mean?

defaultIgnoreParams

and

ignoreParams

Hmmm they should be merged 🤔

the

before

and

after

for the

help

section are great. we should put the nf-core logo there and put a link: if you need further assistance visit the nf-core slack or reachout on github

I gotta go now but please keep reporting all your issues, I'll address them next week

enjoy your weekend

Thank you! You too 😛