OpenSWATH Snakemake Workflows

Installation

Either install all dependencies or use the preconfigured Docker container:

    docker pull openswath/develop:latest

Clone the repository to your local installation.

Usage

Start up an instance of the Docker container:

    docker run --name osw_wf --rm -v workflows:/data -i -t openswath/develop

Copy your DIA files to dia_data.
Edit the parameters in wf_diau, wf_library and wf_openswath if necessary.
Execute the full workflow:

    snakemake -j4