Hi everybody, I'm interested in making some nf-core modules for the new autocycler tool rrwick/Autocycler: A tool for generating consensus long-read assemblies for bacterial genomes • Is anybody already working on this? (I don't see any issues in Issues · nf-core/modules) 🛠️ • Are you interested in helping?/have any recommendations 🎉 • Would this be useful for you? 😄

I'm not working on this, but I do have ideas. In essence, autocycler subsamples reads into multiple files. Those files are then assembled with multiple assemblers. If you put all the assemblers with helper scripts into a container, you will be creating a massive container. It would be better to create a container for each assembler + Autocycler's helper scripts. (As a side note, the helper scripts aren't really needed and workflows using autocycler don't have to be limited to assemblers with helper scripts.) After assembly, autocycler takes the drafts, compares them, and reconciles differences. What I would do, is create modules for the non-assembly autocycler steps, and then encourage users to use modules specific for the assemblies they want to generate for comparison.

Thanks 🙂 I agree, I'm leaning towards separate modules for each step (ignoring assembly) subsample, compress, cluster, trim, resolve, and combine