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.
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README |