This repository contains an ATAC-Seq pipeline using Snakemake.

Folders and files should be self-explanatory, however, a few notes:
  1) The doc folder contains various documentation. The "old" subfolder is messy and can be safely ignored. See the Documentation.pdf for a (beta) version of the documentation.
  2) The example folder is important. Use this to test if you run the pipeline using a small example analysis consisting of two samples. To run it, adjust the parameters in the input/config.json and input/params.sh and input/cluster.json files accordingly.
  3) The src folder contains the source of the project. The R subfolder can be ignored, as we switched completely to Snakemake.