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Add manifest.diagram to config - #1915

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ewels wants to merge 7 commits into
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ewels:manifest-diagram
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Add manifest.diagram to config#1915
ewels wants to merge 7 commits into
nf-core:devfrom
ewels:manifest-diagram

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@ewels

@ewels ewels commented Sep 9, 2026 •
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Getting ahead of the template, but see nf-core/tools#4460 for context.

Adds the manifest.diagram config attribute to point to the metro map.

Also regenerates the metro maps and updates the contributing documentation. Proposed commands depend on seqeralabs/nf-metro#1970 being merged and released (fine to merge here I think as these are read-only for future devs).

New SVG is now automatically supports light+dark mode natively, so renamed and removed some files.

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github-actions Bot commented Sep 9, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

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github-actions Bot commented Sep 9, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9a00169

+| ✅ 213 tests passed       |+
#| ❔  22 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnaseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnaseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_nf_test - actions_nf_test
  • modules_config - modules_config
  • container_configs - container_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-09-10 13:03:32

@ewels
ewels requested a review from pinin4fjords September 10, 2026 12:36
@ewels ewels mentioned this pull request Sep 10, 2026
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ewels
ewels commented Sep 10, 2026
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Comment thread docs/dev/metro_map.md

@ewels ewels Sep 10, 2026

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Can potentially delete this file? Ported most of it the website in nf-core/website#4395

@ewels ewels mentioned this pull request Sep 10, 2026
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@pinin4fjords

pinin4fjords commented Sep 10, 2026

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I'll reconcile this with #1876 soon (which has one or two other things) - please don't merge just yet

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@ewels @pinin4fjords