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StaG Metagenomic Workflow Collaboration (mwc)

DOI Snakemake

StaG mwc logo

The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing a metagenomics analysis workflow suitable for microbiome research and general metagenomics analyses.

Please visit https://stag-mwc.readthedocs.io for the full documentation.

Usage

Step 0: Install conda and Snakemake

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. When running StaG with the --use-conda or --use-singularity flags, all dependencies are managed automatically. If using conda it will automatically install the required versions of all tools required to run StaG-mwc. There is no need to combine the conda and singularity flags: the Singularity images used by the workflow already contain all required dependencies.

Step 1: Clone workflow

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

git clone git@github.com: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.

Step 2: Configure workflow

Configure the workflow according to your needs by editing the file config/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.

Step 3: Execute 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 cluster environment by using one of the available profiles, or creating your own, e.g. to run on CTMR's Gandalf cluster:

snakemake --profile profiles/ctmr_gandalf

Make sure you specify the Slurm account and partition in profiles/ctmr_gandalf/config.yaml. Refer to the official Snakemake documentation for further details on how to run Snakemake workflows on other types of cluster resources.

Note that in all examples above, --use-conda can be replaced with --use-singularity to run in Singularity containers instead of using a locally installed conda. Read more about it under the Running section in the docs.

Testing

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. Suggestions for how to improve the automated testing of StaG-mwc are very welcome!

Contributing

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.

Citing

If you find StaG-mwc useful in your research, please cite the Zenodo DOI: https://zenodo.org/badge/latestdoi/125840716

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Animal vector created by Patrickss - Freepik.com

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