This repo contains the code for a Snakemake workflow of the StaG Metagenomic Workflow Collaboration (mwc). Currently, the project focus is a barebones metagenomics analysis workflow to produce primary output files from several different metagenomic analysis tools.

Go to https://stag-mwc.readthedocs.org for the full documentation.

Conda and Snakemake are required to be able to use StaG-mwc. Most people would probably want to install Miniconda and install Snakemake into their base environment. Conda will automatically install the required versions of all tools required to run StaG-mwc.

To use StaG-mwc, you need a local copy of the workflow repository. Start by making a clone of the repository:

git clone [email protected]:ctmrbio/stag-mwc

If you use StaG-mwc in a publication, please credit the authors by citing either the URL of this repository or the project's DOI. Also, don't forget to cite the publications of the other tools used in your workflow.

Configure the workflow according to your needs by editing the file config.yaml. The most common changes include setting the paths to input and output folders, and configuring what steps of the workflow should be included when running the workflow.

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores N

This will run the workflow locally using N cores. It is also possible to run it in a Slurm-managed cluster environment, e.g. on UPPMAX Rackham:

snakemake --use-conda --profile cluster_configs/rackham

Make sure you edit the Slurm project account in cluster_configs/rackham/rackham.yaml. Refer to the official Snakemake documentation for further details on how to run Snakemake workflows on other types of cluster resources.

A very basic continuous integration test is currently in place. It merely validates the syntax by trying to let Snakemake build the dependency graph if all outputs are activated.

Refer to the contributing guidelines in CONTRIBUTING.md for instructions on how to contribute to StaG-mwc.

If you intend to modify or further develop this workflow, you are welcome to fork this reposity. Please consider sharing potential improvements via a pull request.

If you find StaG-mwc useful in your research, please cite the Zenodo DOI: https://zenodo.org/record/1483891

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