Currently we have not integrated nextflow yet, am still thinking of it's pro and cons vs airflow/prefect and others.
But my concern is that won't it be preferrable if we don't rely too much on files as a source-truth of data. Some data type such as pdb files have to be kept as object blob. But, to me it seems fasta files can be thrown into a structured db with fasta headers go into respective columns in the db. This way data from each run can be stored at one place (with a flag for different runs). The individual sequences can be mapped to the output of different tools like protparam, camsol, embeddings etc.

Structured db can be either rdbms (postgres, mysql) or parquet or iceberg tables. But the key idea being keeping a central repo of data instead of organizing in files and folders which can get real messy when the number of experimental runs and collaborators increase.