Using workflows

Basic usage

To get started with a workflow from the catalog:

  1. Clone the repository or download the specific workflow directory.

git clone https://github.com/<user>/<workflow>

  1. Review the documentation provided with the workflow to understand its requirements and usage.

  2. Configure the workflow by editing the config.yml files as needed.

  3. Create an environment with access to Snakemake. It is recommended to use mamba.

mamba create -n <env-name> -c <channels> snakemake
mamba activate <env-name>

  1. Execute the workflow using Snakemake.

cd <workflow-dir>
snakemake --cores 2

Use the --dry-run option first to check if all inputs are found.

For more detailed instructions, please refer to the individual documentation for each workflow.

Deployment options

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

To run the workflow using apptainer/singularity, use

snakemake --cores all --sdm apptainer

To run the workflow using a combination of conda and apptainer/singularity for software deployment, use

snakemake --cores all --sdm conda apptainer

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow.

For further options such as cluster and cloud execution, see the docs.