Clone
git clone https://github.com/lculibrk/denovo_signature_pipeline/
Build a conda environment from the conda spec file and activate it:
conda create -p ./signature_env --file conda_spec.txt
conda activate signature_env/
Place data in .maf format under data/{project}/genome/cohorts/{cohort}/snv/{sampleid}.maf
Edit the config.yaml file with your specific parameters
Run Snakemake:
snakemake
Alternatively use the launch.sh as a template (or as-is on the GSC servers) to run the pipeline on a cluster:
nohup bash launch.sh 1000 Snakefile &