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refactor: migrate to nf-core-utils plugin#598

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refactor/nf-core-utils-plugin
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refactor: migrate to nf-core-utils plugin#598
edmundmiller wants to merge 1 commit intodevfrom
refactor/nf-core-utils-plugin

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@edmundmiller edmundmiller commented Mar 11, 2026

Summary

  • Replace utils_nfcore_pipeline, utils_nextflow_pipeline, and utils_nfschema_plugin subworkflows with direct imports from nf-core-utils and nf-schema plugins
  • Inline UTILS_NEXTFLOW_PIPELINE, UTILS_NFSCHEMA_PLUGIN, UTILS_NFCORE_PIPELINE calls into PIPELINE_INITIALISATION
  • Delete 3 legacy nf-core subworkflow directories (-1561 lines)

Depends on nf-core/nf-core-utils nf-core-utils@0.5.0 (nf-core/nf-core-utils#33)

Test plan

  • nf-test test tests/default.nf.test --profile test,docker passes (2/2)
  • Verify other test profiles (bismark_hisat, bwameth, bwamem)
  • Verify MultiQC report generation
  • Verify completion email logic still works

🤖 Generated with Claude Code

@edmundmiller @claude
refactor: migrate from legacy subworkflows to nf-core-utils plugin
29efc9c 
Replace utils_nfcore_pipeline, utils_nextflow_pipeline, and
utils_nfschema_plugin subworkflows with direct imports from the
nf-core-utils and nf-schema plugins.

- Inline UTILS_NEXTFLOW_PIPELINE, UTILS_NFSCHEMA_PLUGIN, UTILS_NFCORE_PIPELINE
  into PIPELINE_INITIALISATION
- Import completionEmail, softwareVersionsToYAML, paramsSummaryMultiqc
  from plugin/nf-core-utils
- Remove monochrome_logs take param from PIPELINE_INITIALISATION
- Delete 3 legacy nf-core subworkflow directories
- Clean modules.json entries

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@edmundmiller edmundmiller requested a review from a team as a code owner March 11, 2026 21:50
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nf-core-bot commented Mar 11, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Mar 11, 2026

nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 29efc9c

+| ✅ 234 tests passed       |+
#| ❔   7 tests were ignored |#
Details

❔ Tests ignored:

  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-11 21:52:49

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@FelixKrueger FelixKrueger Awaiting requested review from FelixKrueger FelixKrueger is a code owner automatically assigned from nf-core/methylseq

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@edmundmiller @nf-core-bot