modelblocks-org/module_co2stop_cdr

A module to aggregate European CDR potential from the CO2Stop dataset into flexible spatial resolutions

Overview

Latest release: v0.1.3, Last update: 2026-04-03

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=modelblocks-org/module_co2stop_cdr

Quality control: linting: passed formatting: passed

Topics: carbon-dioxide-removal

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/modelblocks-org/module_co2stop_cdr . --tag v0.1.3

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

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

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

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

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

We recommend consulting the following before using this module:

  • config/config.yaml: a generic example configuration of this module.

  • workflow/internal/config.schema.yaml: a schematic overview of all the configuration options of this module.

  • INTERFACE.yaml: lists module input and output files, and their default locations.

  • tests/integration/Snakefile: an example of how to call this module from another workflow.

This data module is part of the Modelblocks project. Please consult the Modelblocks documentation for more details.

Linting and formatting

Linting results
All tests passed!
Formatting results
All tests passed!