Are there any official nf-core recommendations for using the

params

object in a pipeline? Should

params

only be read in

<http://main.nf|main.nf>

and then passed explicitly into subworkflows, or can subworkflows reference

params

directly?

If I recall correctly, you should not assume the existence of any particular

params

in subworkflows and

params

should only be used in

<http://main.nf|main.nf>

.

I think the stricter Nextflow guidelines that are on the horizon is that params should be read in the main.nf and passed through, not referenced in other places

Definitely makes sense for subworkflows deeper in the pipeline, since they might be reused elsewhere later on. But what about the main pipeline workflow itself? Both #CGFUX04HZ and #CE8SSJV3N reference

params

directly there around 100 times (see here for sarek and here for rnaseq).

yes, you're right this does not apply to

workflows/<PIPELINE_NAME>/main.nf

. Most pipeline use

params

there because the execution of the workflow in that file is enforced through the top level

<http://main.nf|main.nf>

and we thus assume named

params

to be available there. So I'd say its allowed to use

params

in

workflows/<PIPELINE_NAME>/main.nf

.

Same here. Has any blog post or other info been released about it yet?

I think @Simon Pearce is talking about: https://nextflow.io/docs/latest/strict-syntax.html#using-params-outside-the-entry-workflow

I feel quite strongly that the standards are a good idea. Modules and subworkflows should be better encapsulated and not refer directly to params

Is this not already a guideline? modules and subworkflows should not declare params inside 🤔

Yes modules/subworkflow must not have parameters In terms of pipeline entry point we have not updated our guidance yet but come in the near future™️

I totally agree on modules/subworkflows, but that was not the question here. Its about the entry workflow in nf-core pipelines. We usually have

<http://main.nf|main.nf>

(e.g. https://github.com/nf-core/rnaseq/blob/master/main.nf) in the top which includes the actual core workflow in

workflows/<PIPELINE_NAME>/main.nf

. And most of our pipelines use

params

in

workflows/<PIPELINE_NAME>/main.nf

which is discouraged by the new Nextflow guidelines .

I think this is an oversight for rnaseq and sarek and probably needs to be corrected.

On it, but it's a long process

That's what I mean @Felix Kummer we will evenutally move to that, but we don't have guidance on that. So IMO I think if you want to go params all as entry points that's completely fine as 1. we don't have explicit guidance to not do this, 2. it is encouraged Nextflow best practise.

For me we at nf-core should represent the big Nextflow side of @Rob Syme / @Esha Joshi continuum. So we should thrive to be THE BEST PRACTICES