From 3879bd86b6a799e70c19832ad8813612d4516b64 Mon Sep 17 00:00:00 2001 From: Jeffrey Grover Date: Wed, 7 Aug 2019 01:29:23 -0700 Subject: [PATCH] Updated README --- README.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 151be38..a6c6735 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,19 @@ # WGBS Snakemake Workflow This workflow is designed to run the basic steps for a whole-genome bisulfite sequencing experiment. It's intended to automate the workflow for future-use and -reproducibility. If you're looking for something which will do literally -everything for an experiment then this isn't the workflow you're looking for -(yet). However, if you're comfortable running the individual programs and want -to save yourself the trouble of running every step separately this will save you -time. +reproducibility. Its design is explicitly simple to make it easy for users to not +only understand the order and purpose of each step, but to be able to look at the +code and figure out how it works and get it running extremely easily. -The advantage of running this through Snakemake is that it intelligently handles +One advantage of running this through Snakemake is that it intelligently handles threading and replaces completed processes up to the number of cores specified at run-time. Individual options for the steps are mostly hard-coded, as this is intended for reproducibility of our particular workflow. However, options for -the thread count for each step are changeable from the .yaml file. +the thread count for each step are conigurable in the .yaml file. ## Getting Started Edit the .yaml file to include your sample IDs (excluding extensions, -pair numbers, lane info, etc.) and an already bwameth-indexed reference genome. +pair numbers, lane info, etc.) and a reference genome (which may be pre-indexed). Currently, the workflow expects an R1 and R2 file for each sample. Place the individual .fastq.gz files for R1 and R2 into the input_data directory. Once