Dear all, are there nextflow tools which, starting...
# nostupidquestions
a
Dear all, are there nextflow tools which, starting from a pipeline's generic nextflow.config, provide the ability of creating a custom nextflow.config file via web form? I was wondering if the information provided in the nextflow_schema.json can be reused to render the help text and organize the interactive options of the form. The question comes from the fact that, often times, the pipelines that I write are used by technical staff that doesn't necessarily feel comfortable checking a nextflow.config or a nextflow_schema.json. The idea would be to let them configure a pipeline starting from the defaults and help text already set in the nextflow.config/nextflow_schema.json
p
There's a CLI command
nf-core launch
which has both a CLI wizard or can use a web launch form
That works for any Nextflow pipeline with a schema (or even without)
nf-core pipeline pages also have a "Launch" button, eg nf-co.re/genomeqc/1.0.0 -> nf-co.re/launch?pipeline=genomeqc&release=1.0.0 Though this is one of the few things still running on the (very) old nf-core website infrastructure. It needs rewriting really, so not sure how much I'd rely on it.
Then there's also Seqera Platform which does exactly this
But in short, yes: this is one of the main reasons we created
nextflow_schema.json
in the nf-core community back in 2020ish
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a
Thank you, Phil! I'll try nf-core launch
p
Great! Shout if you hit any issues:
nf-core launch
uses the same old website for the web entry, but is functional as far as I know
Should rebuild it really 🤔
Are your users happy with running the CLI command? It's just messing with the parameters etc?
You may also find github.com/ewels/nf-docs useful for generic Nextflow pipelines (nf-core pipelines have their website docs already which basically have the same info)
a
Hi Phil, I'm sorry I could not come back to you earlier! Yes, my users are also fine with CLI tools 🙂 Thank you very much, I'll check your nf-docs as well
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p
Sounds good! Let me know how you get on. That launch website really needs replacing, I've been meaning to do it for years now lolsob
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