Welcome to Snakemake-RNASeq-Workflows’s documentation!

Workflows may contain modified parameters, Please look at snakemake files before use.

Currct workflows

Quick start

1. Prepare samples directory properly

Before you run write_sample_to_json.py, samples directory arangement and it’s naming needs to be proper such that it can be read by the script and call furthere in snakemake files.

Something like this:

2. Generate samples.json file

This will be used to automatic detect samples names and call them in snakemake files.

3. Run Workflows

First Edit the config.yml files inside workflow directory with required full paths.

Then simply call snakemake from workflow directory (With additional parameters if required)


For checking workflow and debug

Visualise the workflow

Indices and tables