Simple Snakemake example
This repo is intended as an easy-to-use starting point for making a quick reproducible bioinformatics analysis using Snakemake.
- Clone the repo to create your analysis folder
git clone git@github.com:ctmrbio/sm3 my_analysis
- Modify the Snakefile according to your needs. Add rules to produce output
files and add desired final output files to the
allrule. - Define the environment required to run the rules in
workflows/envs/conda.yaml. - Create an
inputdirectory and put your input files there (a symlink usually works fine).
Run the workflow locally:
snakemake --use-conda --jobs 10
Run the workflow using Slurm on Gandalf:
snakemake --use-conda --profile profiles/ctmr_gandalf
git clone git@github.com:ctmrbio/sm3
cd sm3
ln -s example_input input
snakemake --use-conda --jobs 1