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Thursday, June 30, 2016

How to deal with paired samples for snakemake

I am currently experimenting snakemake for pipelines. We will have paired samples when processing data. e.g. ChIP-seq (IP vs Input), DNA-seq (Normal vs Tumor). How to specify them in snakemake?
The trick is to use a python dictionary to pair samples and a function to define Input files.

I will show an toy example with ChIP-seq processing.