This is a small release of nf-core/tools: mostly template maintenance and bug fixes, plus pipeline metro map support and a new helper command for container configs.

As always, if you have any problems or run into any bugs, reach out on the #tools slack channel.

Highlights

• Metro maps with manifest.diagram: define your pipeline’s metro map in nextflow.config.
• nf-core pipelines containers create-configs command: regenerate the conf/containers_*.config files on demand.

Metro maps with manifest.diagram

Nextflow 26.10.0 added a manifest.diagram field, which points to a workflow diagram of the pipeline. This makes it easier for other tools to pick up the metro maps, e.g. the RO-crates or Seqera Platform The template now has a commented-out manifest.diagram in nextflow.config, ready for your metro map:

manifest {
    ...
    // diagram = 'docs/images/metro_map.svg'
}

The nextflow_config lint test warns if manifest.diagram is not set, but no pressure if you don’t want to add one (even if all the cool kids do it). If it is set, it must be a relative path to an existing image file inside the pipeline (.svg, .png, .jpg, .jpeg, .gif or .webp), or the test fails. Older Nextflow versions ignore the field, so you can set it now.

Don’t have a metro map yet? See all the ways to create one in the workflow schematics docs.

nf-core pipelines containers create-configs command

nf-core pipelines lint regenerates the conf/containers_*.config files, but it refuses to run on a git tree with uncommitted changes. That is a good safety net in general, but can be annoying. The new command directly regenerates these files on demand:

nf-core pipelines containers create-configs

Miscellaneous

• ext.use_gpu has been superseded by Nextflow’s accelerator directive. We removed it from the process_gpu label in the template, and it is no longer a permitted ext key in module linting. Use task.accelerator instead, as described in the docs.
• nf-schema is bumped to 2.7.3, which is needed to run pipelines with Nextflow 26.04. The nf-schema version used in the awsfulltest workflow is now pinned as well, to avoid an annoying Missing process or function paramsSummaryLog(...) error.
• The fix_linting.yml workflow is now fix-linting.yml and uses the reusable workflow from the nf-core/actions repository, so the nf-core bot token can’t leak. This was already patched into the main/master branch of all nf-core pipelines, so now the dev branch will also have it.
• workflow.onComplete no longer waits for the MultiQC report. If no report was produced, the pipeline doesn’t hang at the end anymore.
• nf-test files are now git-ignored in the template.
• The template’s VS Code settings now recommend useful extensions for contributing to nf-core.
• strandedness is now a permitted meta key in module linting (again).

Changelog

You can find the complete changelog and technical details on GitHub.

Published on

21 October 2026

Written by

@mashehu