Creating pipelines is still a problem. Typically one needs to call a bunch of other tools in order to get to the final result. There could be map/reduce behavior in the middle where chunks of data are processed in parallel in order to gain speed. And you need some kind of data management/tracking as well (putting samples in groups, ingesting raw data, exporting results). And sane monitoring especially if something breaks/fails.
There are probably 100s of tools written for this but no clear winner so far. The traditional software engineering approaches like git, ci/cd seem too heavyweight (or rather too low-level) especially during development. IMHO there could be space for a fully remote/cloud solution where one would code/debug/deploy from the browser optimized for writing/maintaining pipelines.
