use snakemake wrappers and/or contribute to Snakemake workflows

[dlaehnemann]

@jafors just pointed me to this workflow and your paper, @a-h-b. Very impressive workflow (and very cool logo!;).

He also remembered, that we recently had a lot of dada2 wrappers added to the snakemake wrappers (in case you haven't seen this project, yet, it's simply reusable and reproducible building blocks for snakemake workflows, including environment definitions and sometimes dedicated input/output handling). @cpauvert contributed those wrappers and even included dada2 meta-wrappers that chain together many of the individual wrappers in something of a subworkflow. From the discussions on these, I remembered he was also planning to create a workflow at some point. So maybe this could be a good fit to team up and use these wrappers in dadasnake?

And if you feel like even more standardisation and sharing with the workflow, have a look at the snakemake workflows project. That's intended as a growing library of standardized, easy-to-use snakemake worfklows, so dadasnake looks like a perfect fit.

[a-h-b]

Hi David - thanks for the pointers. I'll take a look and come back to you. -AHB

[cpauvert]

Thanks for the introduction here @dlaehnemann. The wrappers I contributed to were initially meant for my small scale use and the workflow I gave a thought is far from being as advanced and mature as what you @a-h-b did with dadasnake. So don't take any offense from this minor alternative I suggested :) If you plan to follow up on David and Jan's ideas, I might be available for some contribution, if you want you could notify me. Best, Charlie

[a-h-b]

Hi Charlie - I really appreciate the idea of using the dada2 wrappers. It's how snakemake is intended, so it's definitely a great idea. I'll take a look at your wrappers as well as some of the other tools' and keep you in the loop for further developments :-) - AHB