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naobservatory / mgs-workflow

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Implement nf-core best practices #13

Open willbradshaw opened 1 month ago

willbradshaw commented 1 month ago

nf-core offers a lot of best practices and associated tooling for developing new pipelines, which we've mostly ignored in the current pipeline. I would like to rework the pipeline to be compatible with nf-core best practices.

willbradshaw commented 1 month ago

This would be a large change that would probably merit a major version increment (to 3.x). I'm not planning to do this in the near future but I think it would pay off pretty quickly once we have time to implement.

willbradshaw commented 1 week ago

I've partially done this in the new version of the pipeline currently available at the dev branch, in that I've implemented modules and subworkflows and restructured the main workflows to use them.

There are a lot of other nf-core features that the pipeline still isn't using, because I decided it would be too much work to implement them right now. I still think many of these are very worth having and will come back to this in the future.