A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi,
I would like to know what to do with all the modules that use `shell` (deprecated) and `template` when some variable are not used in the `<http://main.nf|main.nf>` .
We discussed with @Maxime that the bin folder could be a solution.
What do you think ?

Here is the linked PR for sratools
<https://github.com/nf-core/modules/pull/10109/>

That's what Maxime told me.
What could be really nice would be for template to accept arguments like
`template "detect_ncbi_settings.sh" "${args}"`

What's the reason for it to require wave containers?

Wasn't modules binaries requiring fusion?

I was about to ping <@UPC8CHDKQ> but she is already replying

No just wave: <https://www.nextflow.io/docs/latest/module.html#module-binaries>

but still question remains if we want to rely on the service for standard communnity modules. In that past we have said no, because it means users possibly need to set up something else. I also don't know how this works with running offline...

<@U03SLE7RBAS> your favorite topic

For on-prem servers it doesn't need Wave, just cloud execution

&gt;  What's the reason for it to require wave containers?
Paolo

ah you are right, I missed the line about the local file system

&gt; Paolo
And how can I convince him to drop that requirement? :sweat_smile:

I think it is because the file from the bin folder is copied into the container directly

but you don't need wave to do that :sweat_smile:

The workflow bin dir mechanism is some sort of unsatisfactory hack apparently, which we can't extend to module bin

That's too bad to hear. But it's not too important to me right now :stuck_out_tongue: The regular bin folder is doing enough

I'm wondering if file staging isn't an option to just put the scripts in the bin folder inside of the process execution env

Some Ben + Phil related discussion: <https://nfcore.slack.com/archives/C04QR0T3G3H/p1769684050159159?thread_ts=1769678574.070939&amp;cid=C04QR0T3G3H>

I don't like the principle of a language feature not working without Wave, but i'm not winning the argument

Thanks this helped me understand the problem a bit better :slightly_smiling_face:

Module binaries don’t need Fusion, but the user needs to add a flag in their pipeline code

So, how should I solve linting for `shell`  and missing variable usage with `template` ?