DMS-pipeline

DMS-pipeline is a Nextflow pipeline for processing deep mutational scanning (DMS) data. This pipeline implements the sample processing and analysis by Gianmarco Meier et al. For the original code, please see Gianmarco's repo DMS_ABC.

Running the pipeline

1. Clone the repository.
2. Create or edit a new parameter file e.g. LmrCD.json.
3. Edit the run_DMS-pipeline.slurm script and referer to the respective parameter file.
4. Run the pipeline on the cluster: sbatch run_DMS-pipeline.slurm

Note

You can also perform a dry-run of the pipeline locally with ./run_DMS-pipeline.stub.