loosolab/denis — reverse-engineered prompt

I want this repo turned into a runnable workflow for de novo motif discovery from ATAC seq data. It should take continuous binding scores from one condition or compare two conditions, find footprints across the genome, pull out the relevant sequences, and do iterative motif discovery on the footprints that are not already explained by known motifs.

After that, please make sure it runs the useful follow up analyses too, like comparing discovered motifs to a motif database, checking enrichment in open chromatin, annotating motif sites to genes, and doing gene ontology enrichment from those annotations. I also want the included example to run cleanly so I can test everything first, then switch to my own settings in config.yml.

Please keep the workflow easy to start with one command using the existing workflow setup and conda or mamba, and make the outputs land in the expected numbered result folders with clear notes on what each folder means. If you need details, look up the current docs online.