Seqera Containers migration

Edit

This project continues the ongoing migration of nf-core modules from BioContainers to Seqera Containers, built using Wave.

The migration enables automatic multi-architecture container builds (linux/amd64 and linux/arm64), Conda lock files for improved reproducibility, and prepares the modules for fully automated update pipeline via Renovate and GitHub Actions.

Resources:

• Blog: Migration from Biocontainers to Seqera Containers — Part 2
• nf-core/tools PR #3954
• nf-core/tools PR #3955
• Bulk module update tracker (nf-core/modules #6698)
• Container conversion stats dashboard

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Goal

Migrate nf-core modules and pipelines to use Seqera Containers:

• Modules: build new containers with nf-core modules containers create, and let the tool update meta.yml and main.nf automatically.
• Pipelines: update installed modules and let nf-core modules update auto-generate the per-platform container config files in conf/.
• tools: Add missing functionality for the above goals and fix any related bugs.

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Tasks

Convert a module to Seqera Containers

1. Claim an open module by opening a PR and assigning yourself to it.

2. Run the following nf-core command to build containers via the Wave API and update meta.yml and main.nf automatically:

   nf-core modules containers create <module_name>

   This builds Docker and Singularity images for both linux/amd64 and linux/arm64, writes the image URLs and build IDs into meta.yml, and updates the container string in main.nf.

   Info

   Depending on the current build work load and size of the container, this can take several minutes.

   Note

   Set TOWER_ACCESS_TOKEN to your Seqera Platform token to avoid strict Wave API rate limits.

3. Verify the changes look correct, run tests, and open a Pull Request.

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Update a pipeline to use Seqera Containers

Once modules have been converted, pipelines can adopt the new containers by updating their installed or local modules. The new tooling then auto-generates per-platform container config files under conf/ using nextflow inspect.

1. Inside a pipeline repository, update one or more modules:

   nf-core modules update <module_name>
   # or update all modules at once:
   nf-core modules update

2. The tool automatically runs nextflow inspect and writes config files for all supported platforms:

   Note

   This requires Nextflow >= 25.04.4.

3. Review the generated config files, run the pipeline tests, and open a Pull Request.

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Recommended preparation

Participants should ideally have:

• Basic familiarity with Git and GitHub (forking, branching, pull requests)
• Basic knowledge of Nextflow and nf-core modules or python