Can you describe a scenario that would be impossible to code for in a snakemake paradigm? For example at least with conditionals I imagine you could bake some flags into the output filename and have different jobs parse that. I’m not sure exactly what you mean by loop but if its iterating over something that can probably be handled with the expand or lambda functions.
Here is a scenario which is relatively trivial in Nextflow and difficult to write in snakemake:
1. A process that "generates" protein sequences
2. A collection of processes that perform computationally intensive downstream computations
3. A filter that decides, based on some calculation an a threshold whether the output from process (1) should move to process (2).
Furthermore, assume you'd like process (1) to continue generating new candidates continously and independently until N number of candidates pass the filter for downstream processing.
That's not something that you can do easily with snakemake since it generates the DAG before computation starts.
Sure, you can create some hack or use checkpoints that forces snakemake to reevaluate the DAG and so on, and maybe --keep-going=true so that it won't end the other processes from failing, but with nextflow you just set a few channels as queues and connect them to processes, which is much easier.
Just make your N number of candidates check generate some empty file after N is reached and put that as input for the next job. For threshold example you can do the same thing or even bake the metric into a filename.
As I said, you can hack your way through snakemake to make it work probably using DAG reevaluation and tricks with filenames, but Nextflow allows it in a much more straightforward manner that's more easy to follow, understand and debug.
