ATAC Conditional Rules

[schaughencyp]

For ATAC,

The following can be considered to probably be conditional when running the pipeline:

1. Between macs2 and Genrich- Genrich should be default, macs2 should be conditional
2. Between edgeR and deseq2 in the Diffbind rules - Deseq2 should be default, edgeR should be conditional.
3. Motif analysis (MEME/Homer? rules) could probably be conditional for ATAC.
4. Between genes, prot, protsec, protTSS - I think only prot needs to run by default. This should be a selection as the number of total jobs is ballooning in certain circumstances.

These are suggestions not demands,

Paul