Stephan Reichl

Yes sounds good to me =). re docs, here are my most recent notes: In the feature section, describe its capabilities (List what it can do and give an example...

Interaction terms I would ask the user to explicitly put the term from the formula in the column, separated by `|` as indicated by you. For the general implementation, as...

Unsure why you need it, but if you need it, you can just pass it as a `param` from the `config` in the Snakemake rule. Passing, of course, the whole...

yes, good point. should redirect all log to `{log}` directive but without messing with the multiQC setup.

Add check if `$CONDA_PREFIX` is set and error of not with message to set it

idea: consider using Snakemake wrappers https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bio/homer.html

@burtonjake Indeed, as you can see, this has been an issue for us for a while, and I would love to address it. It's not that straightforward because it does...

> I'm also having quite significant issues with HOMER now. This is also just with my own user's instant of the pipeline... did something change recently with our infrastructure? Thanks...

done in integrative recipe, use this code: https://github.com/epigen/MrBiomics/blob/27a8f880649bbd55005687d21bcb6fcd9163a890/workflow/rules/CorcesINT.smk#L80-L99

For GMT databases use this template ```python #### download Enrichr databases #### rule download_Enrichr_databases: output: "resources/Enrichr_databases/{database}.gmt", params: url = lambda w: "https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName={}".format(w.database), resources: mem_mb="1000", threads: 1 conda: "../envs/wget.yaml" log: "logs/wget/download_Enrichr_databases_{database}.log",...