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

nf-core

Per the warning <https://www.nextflow.io/docs/latest/process.html#multiple-output-files|here> I have found that in my `ENSEMBLVEP_VEP` processes I am getting all my extra `vcf.gz` files that are passed as `extra_files` copied back into my task `workDir`. This is not great when running on AWS with S3 `workDir` as it increases copy time and generally costs more. Is there any reason not to change the output channel designations from `path("*.vcf.gz")` to `path("${prefix}.vcf.gz")`?

I don't see any atm :thinking_face: feel free to fix!

yeah go for it, I did this for several other modules

should we generally add this to the guidelines to avoid wild cards in the output? We shoot ourselves in the foot with this a little too often

I was just about to ask the same haha. Given that advice, and the willingness here for that change, I wonder if nf-core should push for using more qualified output globs? It obviously requires more knowledge of what a tool outputs and can break more if different versions do things more differently, but in general I have found `${prefix}*.vcf` (or whatever extension) works well with my local modules 

given it should be caught with the tests on a module change, the blast radius feels pretty contained to me if a tool changes the naming structure on update. <!subteam^S044DU0NG68> :point_up: wdyt?

Update it. There's also a related issue on Nextflow: <https://github.com/nextflow-io/nextflow/issues/3995>