quick-start.md

Quick Start Instructions

1. Download this repo with one of these methods:

   • Clone:

     git clone https://github.com/SchlossLab/mikropml-snakemake-workflow
     cd mikropml-snakemake-workflow

   • Use this template:

     If you're viewing this on GitHub, click the green Use this template button to create your own version of the repo in your own GitHub, then clone your repo.

2. Install the dependencies.

   1. If you don't have conda/mamba yet, we recommend installing Mambaforge.

   2. Create a conda environment with snakemake installed:

      mamba env create -f workflow/envs/smk.yml
      mamba activate smk

   • Alternatively, you can install the dependencies listed in the conda environments however you like.

3. Edit the configuration file: config/config.yaml.

   See config/README.md for a description of the configuration options.

4. Do a dry run to make sure the snakemake workflow is valid.

   snakemake -n

5. Run the workflow.

   Run it locally using 2 cores:

   snakemake --use-conda --cores 2

   Or specify a different config file:

   snakemake --use-conda --cores 2 --configfile config/test.yaml

   You can use singularity with:

   snakemake --use-singularity --use-conda --cores 2

   Or submit the jobs to a slurm cluster:

   snakemake --profile config/slurm --use-singularity--use-conda 

   See the slurm config instructions for more details on slurm configuration.

6. View the results in report.md (see example here).

   This example report was created by running the workflow on the Great Lakes HPC at the University of Michigan.