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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
Dry-run

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​

To be added.