Using Seqera Containers

Seqera Containers simplifies the container creation process for nf-core modules. Currently, nf-core supports Seqera Containers as an alternative to the default biocontainers source. In the future, Seqera Containers will become the default source for all nf-core module containers. For more information, see the nf-core blog post.

Follow these steps to obtain both Docker and Singularity containers from the Seqera Containers website and configure your modules for integration with nf-core workflows.

  1. (Optional but recommended) Test the environment.yml file locally to ensure that all packages and their versions are compatible:

    conda env create -f environment.yml

  2. Open the Seqera Containers website.

  3. In the search bar, add all the required packages. You can copy and paste entries directly from your environment.yml file (for example, conda-forge::<TOOL>=<VERSION>) to ensure that the correct channels and versions are used.

    Warning

    nf-core modules SHOULD include only a single tool and its required dependencies. Only add additional tools when necessary.

  4. Set Container setting to Docker.

  5. Select Get Container.

  6. Copy the generated container URL and add it to the last line of the container definition in your module’s main.nf file.

    Note

    The URL does not include https:// at the beginning. Copy it exactly as shown.

  7. Change the Container settings to Singularity.

  8. Select Get container.

  9. ❕ Select the HTTPS checkbox.

    Note

    This checkbox appears only after the container has been successfully built.

  10. Copy the generated URL (including the https://community-cr-prod... prefix) and add it to the middle line of the container definition in your module’s main.nf file.