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.
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.
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.
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.
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.
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!
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/badge/latestdoi/125840716