Quickstart

Clone the repo 

git clone https://github.com/bibymaths/grmap
cd grmap

Edit config.yaml

  • Set read to your reads pattern.
  • Point reference, annotations, scripts_dir, and results_dir to the correct paths.

Create your environment

conda create -n grmap -c conda-forge -c bioconda snakemake matplotlib numpy=1.26
conda activate grmap 
sudo cpan Parallel::ForkManager IO::Uncompress::Gunzip

Run the pipeline

snakemake --cores 1 --report results/report.html --report-after-run