Housekeeping

[FriederikeHanssen]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[maxulysse]

I don't think the .bigWig should be here, I think it was better with it on the script part.
But this is probably an issue to report in the modules repo

[FriederikeHanssen]

hm this is the default file ending I choose. apaprently the tool infers whether it is a bedgraph or bigwig file based on file ending provided. I iwll check again if there is a default the tool sets itself

[maxulysse]

Any case, this issue should be resolved on the modules repo, not here, but I can make an issue there so we don't forget if you'd like

[maxulysse]

but then given your answer, and how you already wrote the modules, I would definitively remove the .bigWig part from the whole module and only have that as a prefix and test with both bedgraph and bigwig

[FriederikeHanssen]

ok sure, my thought there was that we have other modules where a prefix is not mandatory. But am happy to have it mandatory here then. not a hill i am going to die on 😆

[maxulysse]

oh I see, then you would want that as an input?

[maxulysse]

maybe definitively we should start a PR for this modules and discuss it with more people.
I'd be happy to die on another hill that this one too

[FriederikeHanssen]

sure sounds good. It would just need to be set in the modules.config under prefix always and thats it. The documentation is not super clear though on what a default value would be. There is also another parameter that can be used to set the output file format. Maybe there could be weird effects, like setting --outputfileformat in args but then not having the corresponding ending in prefix 🤔

ok...yes the more I write about it, the more I am sure it could use some more thought

[maxulysse]

I'm guessing we don't have json args validation yet for modules

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