hassanfa/snakemake_tutorial

Requirements

Make sure you have conda installed.

Step 1: Create a conda environment

conda create -n cg_development_day -c bioconda -c conda-forge python=3.6 pip

Step 2: Activate conda environment

conda activate cg_development_day

Step 3: Install all Snakemake dependencies via pip

pip install -r requirements.txt 

Conda stuff

Step 1: Install required softwares

conda install -c bioconda -c conda-forge vardict-java bcftools samtools bwa rtg-tools

Step 2: Run workflow

snakemake --cores 2 -p

Step 3: Generate a report

snakemake --report && open report.html