good catch @kjellinjonas
could you update the CHANGELOG please?

@nvnieuwk is there a way to have a file be optional, but if it is selected check that it exists before doing anything?

Yes that's the expected behaviour. The plugin will ignore all validation if an optional file has not been given. However when the file has been given, it will do the full validation

ok so removing exists will do exactly that?

This should be solved on a pipeline level IMO, the plugin is doing what it needs to do here.

So either @kjellinjonas adds this file to the local igenomes base path (which I assume here since the germline resources path for example should exist on the s3 bucket)

Or the pipeline gets updated so that these parameters only get populated when they are needed.

(The first option sound the most logical to me, but I'll leave that up to you)

ok so removing exists will do exactly that?

removing exists will just ignore the existence check, do you want that in this case?

Sure, I could add the files. However, I think it's annoying for more people than me if the pipeline requires files to be present that will not be used.

How about keeping these changes, but add additional input checks in the samplesheet_to_channel/main.nf

something like:

if (tools && tools.split(',').contains('ngschekmate')) {
        if (!ngscheckmate_bed) {
            error("No bed file was provided for running NGSCheckMate.")
        }

@FriederikeHanssen @maxulysse

wait, I guess this would only check if the parameter is set and not if the file exists..

Option 2 would be better here then, those params shouldn't be automatically filled in if they are not being used.

Not sure how to achieve that though.. Can parameters be set conditionally in igenomes.config ?

These parameters are set in main.nf using getGenomeAttributes, but please discuss this with the Sarek devs first which method they prefer :)

Sure, I could add the files. However, I think it's annoying for more people than me if the pipeline requires files to be present that will not be used.

How about keeping these changes, but add additional input checks in the samplesheet_to_channel/main.nf

something like:

if (tools && tools.split(',').contains('ngschekmate')) {
        if (!ngscheckmate_bed) {
            error("No bed file was provided for running NGSCheckMate.")
        }

I like where this is going.

But I think it feel like overcharging the samplesheet_to_channel/main.nf.
How about we create a separate subworkflow to check out all these tools and files combinations?

Sounds good to me. However, there are currently several similar checks in samplesheet_to_channel/main.nf (e.g. checking for missing files when mutect2 is used).

So if we create a new subworkflow, I think we can move those checks as well to make it consistent.

Sounds good to me. However, there are currently several similar checks in samplesheet_to_channel/main.nf (e.g. checking for missing files when mutect2 is used).

So if we create a new subworkflow, I think we can move those checks as well to make it consistent.

Make it consistent, that's my life motto

Should I start the work on a new subworkflow here, or should a separate issue/PR be made for that? @maxulysse

Should I start the work on a new subworkflow here, or should a separate issue/PR be made for that? @maxulysse

I'd say let's do it here, that would simplify your work, right?

In utils_nfcore_sarek_pipeline, checkPathParamList is defined and some parameters are only added if the relevant tool is used. To me this looks like a good way to define which parameters to evaluate, but I can't see that this list is actually used anywhere. Am I missing something?

What do you think about this approach? Still a lot to be done (clean up/add test etc.) but it would be great with some input/feedback first

@kjellinjonas maybe for this PR we can fix the issue at hand and split out the refactoring into a different PR since it seems to be a bigger undertaking.

@FriederikeHanssen Sounds good to me. What do I need to do?

Remove the changes not related to the schema & changelog