mchowdh200/cancer-sv-pipeline

Cancer SV calling Pipeline

• Currently under construction...

Snakefile located under workflow/. Basic configuration is contained in workflow/conf/config.yaml. Per rule slurm configuration is located in workflow/conf/cluster-config.yaml.

Dependencies

• conda - for a minimal install of conda, check out miniconda

• mamba - drop in replacement for conda's package manager. Used to install snakemake

$ conda install -n base -c conda-forge mamba

• snakemake

$ mamba create -c conda-forge -c bioconda -n snakemake snakemake