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refactor: flatten pipeline assets back to top-level assets/#1852

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pinin4fjords merged 4 commits into
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flatten-pipeline-assets
May 8, 2026
Merged

refactor: flatten pipeline assets back to top-level assets/#1852
pinin4fjords merged 4 commits into
devfrom
flatten-pipeline-assets

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@pinin4fjords pinin4fjords commented May 8, 2026

Summary

workflows/rnaseq/assets/ is moved up to the canonical assets/ directory so the pipeline matches the standard nf-core layout.

Why

nf-core pipelines bump-version only knows about assets/multiqc_config.yml (see bump_version.py). Our config lived at workflows/rnaseq/assets/multiqc/multiqc_config.yml so the tool silently skipped it on every release bump, forcing manual edits to the report_comment URLs (which is exactly the bug @mashehu flagged on #1799 and applauded the manual fix for on #1844). With the file in the canonical location, nf-core pipelines bump-version 3.27.0 now also touches assets/multiqc_config.yml, .nf-core.yml, nextflow.config, and ro-crate-metadata.json in one shot.

What moves

All under workflows/rnaseq/assets/ are now flat under assets/:

  • multiqc/multiqc_config.yml → multiqc_config.yml
  • multiqc/methods_description_template.yml → methods_description_template.yml
  • multiqc/biotypes_header.txt → biotypes_header.txt
  • multiqc/deseq2_clustering_header.txt → deseq2_clustering_header.txt
  • multiqc/deseq2_pca_header.txt → deseq2_pca_header.txt
  • multiqc/sample_status_header.txt → sample_status_header.txt
  • multiqc/strand_check_summary.yaml → strand_check_summary.yaml
  • multiqc/strand_check_composition.yaml → strand_check_composition.yaml
  • rrna-db-defaults.txt → rrna-db-defaults.txt

Path updates in nextflow.config, nextflow_schema.json, workflows/rnaseq/main.nf, and the pipeline initialisation nf-test. Drops the now-redundant multiqc_config: false lint skip and the assets/multiqc_config.yml entry from files_exist in .nf-core.yml.

Test plan

  • nf-core pipelines bump-version 3.27.0 on a checked-out copy of this branch updates assets/multiqc_config.yml (report_comment URLs), nextflow.config, .nf-core.yml, and ro-crate-metadata.json cleanly
  • Pipeline CI green
  • No remaining references to workflows/rnaseq/assets

🤖 Generated with Claude Code

@pinin4fjords @claude
refactor: flatten pipeline assets back to top-level assets/ [skip ci]
2c5a03f 
Move workflows/rnaseq/assets/* up to assets/, drop the multiqc/
subdirectory, and update path references so the pipeline matches the
standard nf-core layout. This unblocks `nf-core pipelines bump-version`,
which only knows about assets/multiqc_config.yml; previously the file
lived at workflows/rnaseq/assets/multiqc/multiqc_config.yml and silently
went untouched on every release bump.

Also drops the now-redundant multiqc_config lint exemption and the
files_exist exemption for assets/multiqc_config.yml from .nf-core.yml.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords pinin4fjords requested a review from mashehu May 8, 2026 15:03
pinin4fjords and others added 2 commits May 8, 2026 16:04
@pinin4fjords @claude
ci: trigger checks
7a60ba1 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(changelog): add entry for #1852
6fdf8e9 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
JoseEspinosa
JoseEspinosa approved these changes May 8, 2026
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LGTM 🎸

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github-actions Bot commented May 8, 2026 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f8889aa

+| ✅ 215 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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 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 base.config: Check the defaults for all processes

❔ 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
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • 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 passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-08 15:18:24

@pinin4fjords @claude
fix(mqc): drop -module suffix from summary/versions section anchors
f8889aa 
nf-core lint's multiqc_config check requires `software_versions` and
`nf-core-<pipeline>-summary` keys in `report_section_order` (no
`-module` suffix). MultiQC accepts both the bare anchor and the
`-module` form for these custom-content sections, so the rendered
report ordering is unchanged.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords pinin4fjords enabled auto-merge May 8, 2026 15:41
@pinin4fjords pinin4fjords merged commit aff708e into dev May 8, 2026
123 of 125 checks passed
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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@pinin4fjords @JoseEspinosa
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