This is a (working) template repository designed for scientific projects where data is processed using Snakemake.
All required tools are automatically installed by Snakemake using conda environments or singularity/apptainer containers, however Snakemake itself needs to be installed first. Load a software module with Snakemake, use a native install, or use the environment.yml file to create a conda environment for this particular project using fx conda env create -n <snakemake_template> -f environment.yml.
Adjust the config.yaml files under both config/ and profiles/ accordingly, then simply run snakemake --profile profiles/<subfolder> or submit a SLURM job using the slurm_submit.sbatch example script.
The usage of this workflow is also described in the Snakemake Workflow Catalog.
- Replace
<owner>and<repo>with the correct values in thisREADME.mdas well as in files under.github/workflows/. - Replace
<snakemake_template>with the workflow/project name (can be the same as<repo>) here as well as in theenvironment.ymlandslurm_submit.sbatchfiles. - Add more requirements to the
environment.ymlfile if needed, however tools for each Snakemake rule should NOT go here, they should be configured separately for each rule instead inyamlfiles underenvs/. - Fill in fields in this
README.mdfile, in particular provide a proper description of what the workflow does with any relevant details and configuration. - The workflow will occur in the public Snakemake workflow catalog once the repository has been made public and the provided GitHub actions finish correctly. Then the link under "Usage" will point to the usage instructions if
<owner>and<repo>were correctly set. If you don't want to publish the workflow just delete the.github/workflows/and.template/folders andsnakemake-workflow-catalog.yml. - Consider the license - Choose a license
- DELETE this TODO section when finished with all of the above, and then start developing your workflow!