clipkit - new module

[vagkaratzas]

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Closes #XXX

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[nvnieuwk]

Some comments :)

[nvnieuwk]

Maybe rename the clipkit file here to ${prefix}.clipkit that way you are 100% sure it has the correct name

[vagkaratzas]

The default functionality is for the tool to just add ".clipkit" to the input file name. We can either overwrite that within the script by passing the -o argument as suggested ( e.g. ${prefix}.clipkit ) or leave it to the user to do that from a nextflow.config through -args. I left it like this because I thought that just adding a suffix to the filename would be the most wanted functionality. Else to achieve this, the user would need to pass the filename as a meta.id, right?

Which is the preferred nf-core way to do this?

[nvnieuwk]

I'd prefer the -o option to stay consistent with all other modules. The input file name can sometimes be changed by another process in a way that the user doesn't want it. This way you can have full control over the file name in the nf-core best-practice way :)

[nvnieuwk]

LGTM!